Antisense modulation of hematopoietic cell protein tyrosine kinase expression

ABSTRACT

Antisense compounds, compositions and methods are provided for modulating the expression of hematopoietic cell protein tyrosine kinase. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding hematopoietic cell protein tyrosine kinase. Methods of using these compounds for modulation of hematopoietic cell protein tyrosine kinase expression and for treatment of diseases associated with expression of hematopoietic cell protein tyrosine kinase are provided.

FIELD OF THE INVENTION

[0001] The present invention provides compositions and methods for modulating the expression of hematopoietic cell protein tyrosine kinase. In particular, this invention relates to compounds, particularly oligonucleotides, specifically hybridizable with nucleic acids encoding hematopoietic cell protein tyrosine kinase. Such compounds have been shown to modulate the expression of hematopoietic cell protein tyrosine kinase.

BACKGROUND OF THE INVENTION

[0002] Cells in higher animals normally divide only when they are stimulated by growth factors produced by other cells and act by binding to receptor tyrosine kinases on dividing cells. Cancer cells proliferate excessively because, as a result of accumulated mutations, they are able to divide without stimulation from other cells and therefore are no longer subject to normal controls on cell proliferation. The mutated genes which lead to excessive proliferation were originally called oncogenes before their origin as normal genes was understood. The normal genes, from which they arise, are thus often referred to as proto-oncogenes.

[0003] The cellular src gene was the first molecularly-defined proto-oncogene and its product, Src, is now known to be the source of the first detected tyrosine phosphorylation event. Mutations in the src gene, captured in the genome of Rous sarcoma virus, gave rise to the prototype oncogene v-src. Since the first descriptions of the protein tyrosine kinase activity of v-Src, many other proto-oncogenes have been described (Brown and Cooper, Biochim. Biophys. Acta., 1996, 1287, 121-149).

[0004] Intracellular tyrosine kinases can now be divided into at least 8 subfamilies based on catalytic domain sequence similarity and the presence or absence of other functional domains. The members of the Src family in vertebrates include Src, Fyn, Yes, Fgr, Hck, Lck, Blk and Yrk (Brown and Cooper, Biochim. Biophys. Acta., 1996, 1287, 121-149).

[0005] Hematopoietic cell protein tyrosine kinase (also known as Hck and JTK9) was first cloned in 1987 (Quintrell et al., Mol. Cell Biol., 1987, 7, 2267-2275; Ziegler et al., Mol. Cell Biol., 1987, 7, 2276-2285) and later mapped to chromosome 20q11-q12. The hematopoietic cell protein tyrosine kinase gene has been shown to encode two isoforms, p59^(Hck) and p61^(Hck) which are derived from a single mRNA by alternative initiation of translation (Robbins et al., Mol. Cell Biol., 1995, 15, 3507-3515).

[0006] Hematopoietic cell protein tyrosine kinase expression is highest in differentiated monocytic and granulocytic cells, suggesting that the protein might function in myeloid differentiation or activation (Lichtenberg et al., Oncogene, 1992, 7, 849-858). Taguchi et al. have demonstrated that hematopoietic cell protein tyrosine kinase and Lyn are the major Src-family protein tyrosine kinases expressed in precursor lymphoblastic leukemia cells, the cell type from which childhood leukemia arises most frequently (Taguchi et al., Exp. Hematol. (N.Y.), 2000, 28, 55-64).

[0007] Cartledge et al. have recently generated monoclonal antibodies to murine hematopoietic cell protein tyrosine kinase for the purpose of pursuing investigations of the roles of hematopoietic cell protein tyrosine kinase in signal transduction (Cartledge et al., Hybridoma, 2000, 19, 323-330)

[0008] Hematopoietic cell protein tyrosine kinase has been demonstrated to interact with Bcr-Abl, a constitutively active protein tyrosine kinase expressed as a result of the Philadelphia translocation in chronic myelogenous leukemia. Kinase-defective hematopoietic cell protein tyrosine kinase was found to suppress Bcr-Abl-induced outgrowth of the cytokine-dependent myeloid leukemia cell line (Lionberger et al., J. Biol. Chem., 2000, 275, 18581-18585).

[0009] Investigations of polymorphonuclear neutrophils isolated from mice deficient in hematopoietic cell protein tyrosine kinase and Fgr have identified a role for these Src family kinases in a signaling pathway leading to granule-plasma membrane fusion and have identified Fgr and hematopoietic cell protein tyrosine kinase as potential targets for pharmacological control of the inflammatory process (Mocsai et al., J. Immunol., 1999, 162, 1120-1126).

[0010] Investigations of encephalomyocarditis virus-infected mice treated with the Src kinase inhibitor PP2 have indicated that hematopoietic cell protein tyrosine kinase plays an important role in the activation of macrophages and the subsequent production of tumor necrosis factor-alpha and nitric oxide which lead to the destruction of pancreatic beta cells, leading to diabetes. The inhibition of hematopoietic cell protein tyrosine kinase was found to prevent the onset of diabetes in this study (Choi et al., J. Virol., 2001, 75, 1949-1957).

[0011] Hematopoietic cell protein tyrosine kinase and Fgr double knock-out mice have been found to be resistant to endotoxic shock and exhibit reduced neutrophil migration, indicating that hematopoietic cell protein tyrosine kinase may be an appropriate target for therapeutic intervention in inflammatory diseases (Lowell and Berton, Proc. Natl. Acad. Sci. U.S. A., 1998, 95, 7580-7584).

[0012] Tokunaga et al. have reported inhibition of human immunodeficiency virus type 1 (HIV-1) infectivity by the expression of a dominant-negative hematopoietic cell protein tyrosine kinase protein in T293 cells, indicating a role of Src kinases in regulation of entry of HIV-1 into target cells (Tokunaga et al., J. Virol., 1998, 72, 6257-6259).

[0013] Small molecule inhibitors of Src family tyrosine kinases are well known in the art. Examples include natural products such as radiciol and geldanamycin, ring-fused pyrimidines, benzopyrans and thiol-reactive agents (Showalter and Kraker, Pharmacol. Ther., 1997, 76, 55-71).

[0014] Schindler et al. have reported the crystal structure of hematopoietic cell protein tyrosine kinase in complex with a pyrazolo pyrimidine-type Src family kinase inhibitor known as PP1 (Schindler et al., Mol. Cell, 1999, 3, 639-648).

[0015] A 21-mer antisense phosphorothioate oligonucleotide targeting the seven codons immediately downstream from the translation initiation site of the murine hematopoietic cell protein tyrosine kinase gene has been used to inhibit hematopoietic cell protein tyrosine kinase expression in investigations of tumor necrosis factor production by murine macrophages (English et al., J. Exp. Med., 1993, 178, 1017-1022) and lipopolysaccharide and interferon-gamma-mediated phosphorylation of the proto-oncogene vav (English et al., J. Leukocyte Biol., 1997, 62, 859-864).

[0016] A 20-mer phosphorothioate oligonucleotide targeting the start codon of human hematopoietic cell protein tyrosine kinase was used to inhibit hematopoietic cell protein tyrosine kinase in investigations of neutrophil apoptosis stimulated by granulocyte-macrophage colony-stimulating factor (Wei et al., J. Immunol., 1996, 157, 5155-5162).

[0017] Currently, there are no known therapeutic agents that effectively inhibit the synthesis of hematopoietic cell protein tyrosine kinase. To date, investigative strategies aimed at modulating hematopoietic cell protein tyrosine kinase expression have involved the use of antibodies, small molecule inhibitors and antisense oligonucleotides. Consequently, there remains a long felt need for additional agents capable of effectively inhibiting hematopoietic cell protein tyrosine kinase function.

[0018] Antisense technology is emerging as an effective means for reducing the expression of specific gene products and may therefore prove to be uniquely useful in a number of therapeutic, diagnostic, and research applications for the modulation of expression of hematopoietic cell protein tyrosine kinase.

[0019] The present invention provides compositions and methods for modulating expression of hematopoietic cell protein tyrosine kinase.

SUMMARY OF THE INVENTION

[0020] The present invention is directed to compounds, particularly antisense oligonucleotides, which are targeted to a nucleic acid encoding hematopoietic cell protein tyrosine kinase, and which modulate the expression of hematopoietic cell protein tyrosine kinase. Pharmaceutical and other compositions comprising the compounds of the invention are also provided. Further provided are methods of modulating the expression of hematopoietic cell protein tyrosine kinase in cells or tissues comprising contacting said cells or tissues with one or more of the antisense compounds or compositions of the invention. Further provided are methods of treating an animal, particularly a human, suspected of having or being prone to a disease or condition associated with expression of hematopoietic cell protein tyrosine kinase by administering a therapeutically or prophylactically effective amount of one or more of the antisense compounds or compositions of the invention.

DETAILED DESCRIPTION OF THE INVENTION

[0021] The present invention employs oligomeric compounds, particularly antisense oligonucleotides, for use in modulating the function of nucleic acid molecules encoding hematopoietic cell protein tyrosine kinase, ultimately modulating the amount of hematopoietic cell protein tyrosine kinase produced. This is accomplished by providing antisense compounds which specifically hybridize with one or more nucleic acids encoding hematopoietic cell protein tyrosine kinase. As used herein, the terms “target nucleic acid” and “nucleic acid encoding hematopoietic cell protein tyrosine kinase” encompass DNA encoding hematopoietic cell protein tyrosine kinase, RNA (including pre-mRNA and mRNA) transcribed from such DNA, and also cDNA derived from such RNA. The specific hybridization of an oligomeric compound with its target nucleic acid interferes with the normal function of the nucleic acid. This modulation of function of a target nucleic acid by compounds which specifically hybridize to it is generally referred to as “antisense”. The functions of DNA to be interfered with include replication and transcription. The functions of RNA to be interfered with include all vital functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity which may be engaged in or facilitated by the RNA. The overall effect of such interference with target nucleic acid function is modulation of the expression of hematopoietic cell protein tyrosine kinase. In the context of the present invention, “modulation” means either an increase (stimulation) or a decrease (inhibition) in the expression of a gene. In the context of the present invention, inhibition is the preferred form of modulation of gene expression and mRNA is a preferred target.

[0022] It is preferred to target specific nucleic acids for antisense. “Targeting” an antisense compound to a particular nucleic acid, in the context of this invention, is a multistep process. The process usually begins with the identification of a nucleic acid sequence whose function is to be modulated. This may be, for example, a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state, or a nucleic acid molecule from an infectious agent. In the present invention, the target is a nucleic acid molecule encoding hematopoietic cell protein tyrosine kinase. The targeting process also includes determination of a site or sites within this gene for the antisense interaction to occur such that the desired effect, e.g., detection or modulation of expression of the protein, will result. Within the context of the present invention, a preferred intragenic site is the region encompassing the translation initiation or termination codon of the open reading frame (ORF) of the gene. Since, as is known in the art, the translation initiation codon is typically 5′-AUG (in transcribed mRNA molecules; 5′-ATG in the corresponding DNA molecule), the translation initiation codon is also referred to as the “AUG codon,” the “start codon” or the “AUG start codon”. A minority of genes have a translation initiation codon having the RNA sequence 5′-GUG, 5′-UUG or 5′-CUG, and 5′-AUA, 5′-ACG and 5′-CUG have been shown to function in vivo. Thus, the terms “translation initiation codon” and “start codon” can encompass many codon sequences, even though the initiator amino acid in each instance is typically methionine (in eukaryotes) or formylmethionine (in prokaryotes). It is also known in the art that eukaryotic and prokaryotic genes may have two or more alternative start codons, any one of which may be preferentially utilized for translation initiation in a particular cell type or tissue, or under a particular set of conditions. In the context of the invention, “start codon” and “translation initiation codon” refer to the codon or codons that are used in vivo to initiate translation of an mRNA molecule transcribed from a gene encoding hematopoietic cell protein tyrosine kinase, regardless of the sequence(s) of such codons.

[0023] It is also known in the art that a translation termination codon (or “stop codon”) of a gene may have one of three sequences, i.e., 5′-UAA, 5′-UAG and 5′-UGA (the corresponding DNA sequences are 5′-TAA, 5′-TAG and 5′-TGA, respectively). The terms “start codon region” and “translation initiation codon region” refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in either direction (i.e., 5′ or 3′) from a translation initiation codon. Similarly, the terms “stop codon region” and “translation termination codon region” refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in either direction (i.e., 5′ or 3′) from a translation termination codon.

[0024] The open reading frame (ORF) or “coding region,” which is known in the art to refer to the region between the translation initiation codon and the translation termination codon, is also a region which may be targeted effectively. Other target regions include the 5′ untranslated region (5′UTR), known in the art to refer to the portion of an mRNA in the 5′ direction from the translation initiation codon, and thus including nucleotides between the 5′ cap site and the translation initiation codon of an mRNA or corresponding nucleotides on the gene, and the 3′ untranslated region (3′UTR), known in the art to refer to the portion of an mRNA in the 3′ direction from the translation termination codon, and thus including nucleotides between the translation termination codon and 3′ end of an mRNA or corresponding nucleotides on the gene. The 5′ cap of an mRNA comprises an N7-methylated guanosine residue joined to the 5′-most residue of the mRNA via a 5′-5′ triphosphate linkage. The 5′ cap region of an mRNA is considered to include the 5′ cap structure itself as well as the first 50 nucleotides adjacent to the cap. The 5′ cap region may also be a preferred target region.

[0025] Although some eukaryotic mRNA transcripts are directly translated, many contain one or more regions, known as “introns,” which are excised from a transcript before it is translated. The remaining (and therefore translated) regions are known as “exons” and are spliced together to form a continuous mRNA sequence. mRNA splice sites, i.e., intron-exon junctions, may also be preferred target regions, and are particularly useful in situations where aberrant splicing is implicated in disease, or where an overproduction of a particular mRNA splice product is implicated in disease. Aberrant fusion junctions due to rearrangements or deletions are also preferred targets. It has also been found that introns can also be effective, and therefore preferred, target regions for antisense compounds targeted, for example, to DNA or pre-mRNA.

[0026] It is also known in the art that alternative RNA transcripts can be produced from the same genomic region of DNA. These alternative transcripts are generally known as “variants”. More specifically, “pre-mRNA variants” are transcripts produced from the same genomic DNA that differ from other transcripts produced from the same genomic DNA in either their start or stop position and contain both intronic and extronic regions.

[0027] Upon excision of one or more exon or intron regions or portions thereof during splicing, pre-mRNA variants produce smaller “mRNA variants”. Consequently, mRNA variants are processed pre-mRNA variants and each unique pre-mRNA variant must always produce a unique mRNA variant as a result of splicing. These mRNA variants are also known as “alternative splice variants”. If no splicing of the pre-mRNA variant occurs then the pre-mRNA variant is identical to the mRNA variant.

[0028] It is also known in the art that variants can be produced through the use of alternative signals to start or stop transcription and that pre-mRNAs and mRNAs can possess more that one start codon or stop codon. Variants that originate from a pre-mRNA or mRNA that use alternative start codons are known as “alternative start variants” of that pre-mRNA or mRNA. Those transcripts that use an alternative stop codon are known as “alternative stop variants” of that pre-mRNA or mRNA. One specific type of alternative stop variant is the “polyA variant” in which the multiple transcripts produced result from the alternative selection of one of the “polyA stop signals” by the transcription machinery, thereby producing transcripts that terminate at unique polyA sites.

[0029] Once one or more target sites have been identified, oligonucleotides are chosen which are sufficiently complementary to the target, i.e., hybridize sufficiently well and with sufficient specificity, to give the desired effect.

[0030] In the context of this invention, “hybridization” means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases. For example, adenine and thymine are complementary nucleobases which pair through the formation of hydrogen bonds. “Complementary,” as used herein, refers to the capacity for precise pairing between two nucleotides. For example, if a nucleotide at a certain position of an oligonucleotide is capable of hydrogen bonding with a nucleotide at the same position of a DNA or RNA molecule, then the oligonucleotide and the DNA or RNA are considered to be complementary to each other at that position. The oligonucleotide and the DNA or RNA are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleotides which can hydrogen bond with each other. Thus, “specifically hybridizable” and “complementary” are terms which are used to indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between the oligonucleotide and the DNA or RNA target. It is understood in the art that the sequence of an antisense compound need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable. An antisense compound is specifically hybridizable when binding of the compound to the target DNA or RNA molecule interferes with the normal function of the target DNA or RNA to cause a loss of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed.

[0031] Antisense and other compounds of the invention which hybridize to the target and inhibit expression of the target are identified through experimentation, and the sequences of these compounds are hereinbelow identified as preferred embodiments of the invention. The target sites to which these preferred sequences are complementary are hereinbelow referred to as “active sites” and are therefore preferred sites for targeting. Therefore another embodiment of the invention encompasses compounds which hybridize to these active sites.

[0032] Antisense compounds are commonly used as research reagents and diagnostics. For example, antisense oligonucleotides, which are able to inhibit gene expression with exquisite specificity, are often used by those of ordinary skill to elucidate the function of particular genes. Antisense compounds are also used, for example, to distinguish between functions of various members of a biological pathway. Antisense modulation has, therefore, been harnessed for research use.

[0033] For use in kits and diagnostics, the antisense compounds of the present invention, either alone or in combination with other antisense compounds or therapeutics, can be used as tools in differential and/or combinatorial analyses to elucidate expression patterns of a portion or the entire complement of genes expressed within cells and tissues.

[0034] Expression patterns within cells or tissues treated with one or more antisense compounds are compared to control cells or tissues not treated with antisense compounds and the patterns produced are analyzed for differential levels of gene expression as they pertain, for example, to disease association, signaling pathway, cellular localization, expression level, size, structure or function of the genes examined. These analyses can be performed on stimulated or unstimulated cells and in the presence or absence of other compounds which affect expression patterns.

[0035] Examples of methods of gene expression analysis known in the art include DNA arrays or microarrays (Brazma and Vilo, FEBS Lett., 2000, 480, 17-24; Celis, et al., FEBES Lett., 2000, 480, 2-16), SAGE (serial analysis of gene expression)(Madden, et al., Drug Discov. Today, 2000, 5, 415-425), READS (restriction enzyme amplification of digested cDNAs) (Prashar and Weissman, Methods Enzymol., 1999, 303, 258-72), TOGA (total gene expression analysis) (Sutcliffe, et al., Proc. Natl. Acad. Sci. U.S.A., 2000, 97, 1976-81), protein arrays and proteomics (Celis, et al., FEBS Lett., 2000, 480, 2-16; Jungblut, et al., Electrophoresis, 1999, 20, 2100-10), expressed sequence tag (EST) sequencing (Celis, et al., FEBS Lett., 2000, 480, 2-16; Larsson, et al., J. Biotechnol., 2000, 80, 143-57), subtractive RNA fingerprinting (SuRF) (Fuchs, et al., Anal. Biochem., 2000, 286, 91-98; Larson, et al., Cytometry, 2000, 41, 203-208), subtractive cloning, differential display (DD) (Jurecic and Belmont, Curr. Opin. Microbiol., 2000, 3, 316-21), comparative genomic hybridization (Carulli, et al., J. Cell Biochem. Suppl., 1998, 31, 286-96), FISH (fluorescent in situ hybridization) techniques (Going and Gusterson, Eur. J. Cancer, 1999, 35, 1895-904) and mass spectrometry methods (reviewed in (To, Comb. Chem. High Throughput Screen, 2000, 3, 235-41).

[0036] The specificity and sensitivity of antisense is also harnessed by those of skill in the art for therapeutic uses. Antisense oligonucleotides have been employed as therapeutic moieties in the treatment of disease states in animals and man. Antisense oligonucleotide drugs, including ribozymes, have been safely and effectively administered to humans and numerous clinical trials are presently underway. It is thus established that oligonucleotides can be useful therapeutic modalities that can be configured to be useful in treatment regimes for treatment of cells, tissues and animals, especially humans.

[0037] In the context of this invention, the term “oligonucleotide” refers to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimetics thereof. This term includes oligonucleotides composed of naturally-occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally-occurring portions which function similarly. Such modified or substituted oligonucleotides are often preferred over native forms because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for nucleic acid target and increased stability in the presence of nucleases.

[0038] While antisense oligonucleotides are a preferred form of antisense compound, the present invention comprehends other oligomeric antisense compounds, including but not limited to oligonucleotide mimetics such as are described below. The antisense compounds in accordance with this invention preferably comprise from about 8 to about 50 nucleobases (i.e. from about 8 to about 50 linked nucleosides). Particularly preferred antisense compounds are antisense oligonucleotides, even more preferably those comprising from about 12 to about 30 nucleobases. Antisense compounds include ribozymes, external guide sequence (EGS) oligonucleotides (oligozymes), and other short catalytic RNAs or catalytic oligonucleotides which hybridize to the target nucleic acid and modulate its expression.

[0039] As is known in the art, a nucleoside is a base-sugar combination. The base portion of the nucleoside is normally a heterocyclic base. The two most common classes of such heterocyclic bases are the purines and the pyrimidines. Nucleotides are nucleosides that further include a phosphate group covalently linked to the sugar portion of the nucleoside. For those nucleosides that include a pentofuranosyl sugar, the phosphate group can be linked to either the 2′, 3′ or 5′ hydroxyl moiety of the sugar. In forming oligonucleotides, the phosphate groups covalently link adjacent nucleosides to one another to form a linear polymeric compound. In turn the respective ends of this linear polymeric structure can be further joined to form a circular structure, however, open linear structures are generally preferred. Within the oligonucleotide structure, the phosphate groups are commonly referred to as forming the internucleoside backbone of the oligonucleotide. The normal linkage or backbone of RNA and DNA is a 3′ to 5′ phosphodiester linkage.

[0040] Specific examples of preferred antisense compounds useful in this invention include oligonucleotides containing modified backbones or non-natural internucleoside linkages. As defined in this specification, oligonucleotides having modified backbones include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referenced in the art, modified oligonucleotides that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.

[0041] Preferred modified oligonucleotide backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotri-esters, methyl and other alkyl phosphonates including 3′ -alkylene phosphonates, 5′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, selenophosphates and borano-phosphates having normal 3′-5′ linkages, 2′-5′ linked analogs of these, and those having inverted polarity wherein one or more internucleotide linkages is a 3′ to 3′, 5′ to 5′ or 2′ to 2′ linkage. Preferred oligonucleotides having inverted polarity comprise a single 3′ to 3′ linkage at the 3′-most internucleotide linkage i.e. a single inverted nucleoside residue which may be abasic (the nucleobase is missing or has a hydroxyl group in place thereof). Various salts, mixed salts and free acid forms are also included.

[0042] Representative United States patents that teach the preparation of the above phosphorus-containing linkages include, but are not limited to, U.S. Pat. No.: 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; 5,194,599; 5,565,555; 5,527,899; 5,721,218; 5,672,697 and 5,625,050, certain of which are commonly owned with this application, and each of which is herein incorporated by reference.

[0043] Preferred modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; riboacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH₂ component parts.

[0044] Representative United States patents that teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. No.: 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; 5,792,608; 5,646,269 and 5,677,439, certain of which are commonly owned with this application, and each of which is herein incorporated by reference.

[0045] In other preferred oligonucleotide mimetics, both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative United States patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. No.: 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found in Nielsen et al., Science, 1991, 254, 1497-1500.

[0046] Most preferred embodiments of the invention are oligonucleotides with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular —CH₂—NH—O—CH₂—, —CH₂—N(CH₃)—O—CH₂— [known as a methylene (methylimino) or MMI backbone], —CH₂—O—N(CH₃) —CH₂—, —CH₂—N(CH₃)—N(CH₃)—CH₂— and —O—N(CH₃)—CH₂—CH₂— [wherein the native phosphodiester backbone is represented as —O—P—O—CH₂—] of the above referenced U.S. Pat. No. 5,489,677, and the amide backbones of the above referenced U.S. Pat. No. 5,602,240. Also preferred are oligonucleotides having morpholino backbone structures of the above-referenced U.S. Pat. No. 5,034,506.

[0047] Modified oligonucleotides may also contain one or more substituted sugar moieties. Preferred oligonucleotides comprise one of the following at the 2′ position: OH; F; O—, S—, or N-alkyl; O—, S—, or N-alkenyl; O—, S— or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C₁ to C₁₀ alkyl or C₂ to C₁₀ alkenyl and alkynyl. Particularly preferred are O[(CH₂)_(n)O]_(m)CH₃, O(CH₂)_(n)OCH₃, O(CH₂)_(n)NH₂, O(CH₂)_(n)CH₃, O(CH₂)_(n)ONH₂, and O(CH₂)_(n)ON[(CH₂)_(n)CH₃)]₂, where n and mare from 1 to about 10. Other preferred oligonucleotides comprise one of the following at the 2′ position: C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkenyl, alkynyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, poly-alkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties. A preferred modification includes 2′-methoxyethoxy (2′-O—CH₂CH₂OCH₃, also known as 2′-O-(2-methoxyethyl) or 2′-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78, 486-504) i.e., an alkoxyalkoxy group. A further preferred modification includes 2′-dimethylaminooxyethoxy, i.e., a O(CH₂)₂ON(CH₃)₂ group, also known as 2′-DMAOE, as described in examples hereinbelow, and 2′-dimethylamino-ethoxyethoxy (also known in the art as 2′-O-dimethylamino-ethoxyethyl or 2′-DMAEOE), i.e., 2′-O—CH₂—O—CH₂—N(CH₂)₂, also described in examples hereinbelow.

[0048] A further prefered modification includes Locked Nucleic Acids (LNAs) in which the 2′-hydroxyl group is linked to the 3′ or 4′ carbon atom of the sugar ring thereby forming a bicyclic sugar moiety. The linkage is preferably a methelyne (—CH₂—)_(n) group bridging the 2′ oxygen atom and the 4′ carbon atom wherein n is 1 or 2. LNAs and preparation thereof are described in WO 98/39352 and WO 99/14226.

[0049] Other preferred modifications include 2′-methoxy (2′-O—CH₃), 2′-aminopropoxy (2′-OCH₂CH₂CH₂NH₂), 2′-allyl (2′-CH₂—CH═CH₂), 2′-O-allyl (2′-O—CH₂—CH═CH₂) and 2′-fluoro (2′-F). The 2′-modification may be in the arabino (up) position or ribo (down) position. A preferred 2′-arabino modification is 2′-F. Similar modifications may also be made at other positions on the oligonucleotide, particularly the 3′ position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linked oligonucleotides and the 5′ position of 5′ terminal nucleotide. Oligonucleotides may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative United States patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat. No.: 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; 5,792,747; and 5,700,920, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.

[0050] Oligonucleotides may also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl (—C≡C—CH₃) uracil and cytosine and other alkynyl derivatives of pyrimidine bases, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 2-F-adenine, 2-amino-adenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine. Further modified nucleobases include tricyclic pyrimidines such as phenoxazine cytidine (1H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one), phenothiazine cytidine (1H-pyrimido[5,4-b] [1,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g. 9-(2-aminoethoxy)-H-pyrimido[5,4-b] [1,4]benzoxazin-2(3H)-one), carbazole cytidine (2H-pyrimido[4,5-b] indol-2-one), pyridoindole cytidine (H-pyrido[3′,2′:4,5]pyrrolo[2,3-d]pyrimidin-2-one). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John Wiley & Sons, 1990, those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B. ed., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds of the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., eds., Antisense Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are presently preferred base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications.

[0051] Representative United States patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. Pat. No. 3,687,808, as well as U.S. Pat. No.: 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; 5,645,985; 5,830,653; 5,763,588; 6,005,096; and 5,681,941, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference, and U.S. Pat. No. 5,750,692, which is commonly owned with the instant application and also herein incorporated by reference.

[0052] Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates which enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. The compounds of the invention can include conjugate groups covalently bound to functional groups such as primary or secondary hydroxyl groups. Conjugate groups of the invention include intercalators, reporter molecules, polyamines, polyamides, polyethylene glycols, polyethers, groups that enhance the pharmacodynamic properties of oligomers, and groups that enhance the pharmacokinetic properties of oligomers. Typical conjugates groups include cholesterols, lipids, phospholipids, biotin, phenazine, folate, phenanthridine, anthraquinone, acridine, fluores-ceins, rhodamines, coumarins, and dyes. Groups that enhance the pharmacodynamic properties, in the context of this invention, include groups that improve oligomer uptake, enhance oligomer resistance to degradation, and/or strengthen sequence-specific hybridization with RNA. Groups that enhance the pharmacokinetic properties, in the context of this invention, include groups that improve oligomer uptake, distribution, metabolism or excretion. Representative conjugate groups are disclosed in International Patent Application PCT/US92/09196, filed Oct. 23, 1992 the entire disclosure of which is incorporated herein by reference. Conjugate moieties include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937. Oligonucleotides of the invention may also be conjugated to active drug substances, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fenbufen, ketoprofen, (S)-(+)-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indomethicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic. Oligonucleotide-drug conjugates and their preparation are described in U.S. patent application Ser. No. 09/334,130 (filed Jun. 15, 1999) which is incorporated herein by reference in its entirety.

[0053] Representative United States patents that teach the preparation of such oligonucleotide conjugates include, but are not limited to, U.S. Pat. No.: 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference.

[0054] It is not necessary for all positions in a given compound to be uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single compound or even at a single nucleoside within an oligonucleotide. The present invention also includes antisense compounds which are chimeric compounds. “Chimeric” antisense compounds or “chimeras,” in the context of this invention, are antisense compounds, particularly oligonucleotides, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotide compound. These oligonucleotides typically contain at least one region wherein the oligonucleotide is modified so as to confer upon the oligonucleotide increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid. An additional region of the oligonucleotide may serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. By way of example, RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of oligonucleotide inhibition of gene expression. Consequently, comparable results can often be obtained with shorter oligonucleotides when chimeric oligonucleotides are used, compared to phosphorothioate deoxyoligonucleotides hybridizing to the same target region. Cleavage of the RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art.

[0055] Chimeric antisense compounds of the invention may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonucleosides and/or oligonucleotide mimetics as described above. Such compounds have also been referred to in the art as hybrids or gapmers. Representative United States patents that teach the preparation of such hybrid structures include, but are not limited to, U.S. Pat. No.: 5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711; 5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and 5,700,922, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.

[0056] The antisense compounds used in accordance with this invention may be conveniently and routinely made through the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, Calif.). Any other means for such synthesis known in the art may additionally or alternatively be employed. It is well known to use similar techniques to prepare oligonucleotides such as the phosphorothioates and alkylated derivatives.

[0057] The antisense compounds of the invention are synthesized in vitro and do not include antisense compositions of biological origin, or genetic vector constructs designed to direct the in vivo synthesis of antisense molecules. The compounds of the invention may also be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, as for example, liposomes, receptor targeted molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption. Representative United States patents that teach the preparation of such uptake, distribution and/or absorption assisting formulations include, but are not limited to, U.S. Pat. No.: 5,108,921; 5,354,844; 5,416,016; 5,459,127; 5,521,291; 5,543,158; 5,547,932; 5,583,020; 5,591,721; 4,426,330; 4,534,899; 5,013,556; 5,108,921; 5,213,804; 5,227,170; 5,264,221; 5,356,633; 5,395,619; 5,416,016; 5,417,978; 5,462,854; 5,469,854; 5,512,295; 5,527,528; 5,534,259; 5,543,152; 5,556,948; 5,580,575; and 5,595,756, each of which is herein incorporated by reference.

[0058] The antisense compounds of the invention encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other compound which, upon administration to an animal including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to prodrugs and pharmaceutically acceptable salts of the compounds of the invention, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents.

[0059] The term “prodrug” indicates a therapeutic agent that is prepared in an inactive form that is converted to an active form (i.e., drug) within the body or cells thereof by the action of endogenous enzymes or other chemicals and/or conditions. In particular, prodrug versions of the oligonucleotides of the invention are prepared as SATE [(S-acetyl-2-thioethyl) phosphate] derivatives according to the methods disclosed in WO 93/24510 to Gosselin et al., published Dec. 9, 1993 or in WO 94/26764 and U.S. Pat. No. 5,770,713 to Imbach et al.

[0060] The term “pharmaceutically acceptable salts” refers to physiologically and pharmaceutically acceptable salts of the compounds of the invention: i.e., salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto.

[0061] Pharmaceutically acceptable base addition salts are formed with metals or amines, such as alkali and alkaline earth metals or organic amines. Examples of metals used as cations are sodium, potassium, magnesium, calcium, and the like. Examples of suitable amines are N,N′-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, dicyclohexylamine, ethylenediamine, N-methylglucamine, and procaine (see, for example, Berge et al., “Pharmaceutical Salts,” J. of Pharma Sci., 1977, 66, 1-19). The base addition salts of said acidic compounds are prepared by contacting the free acid form with a sufficient amount of the desired base to produce the salt in the conventional manner. The free acid form may be regenerated by contacting the salt form with an acid and isolating the free acid in the conventional manner. The free acid forms differ from their respective salt forms somewhat in certain physical properties such as solubility in polar solvents, but otherwise the salts are equivalent to their respective free acid for purposes of the present invention. As used herein, a “pharmaceutical addition salt” includes a pharmaceutically acceptable salt of an acid form of one of the components of the compositions of the invention. These include organic or inorganic acid salts of the amines. Preferred acid salts are the hydrochlorides, acetates, salicylates, nitrates and phosphates. Other suitable pharmaceutically acceptable salts are well known to those skilled in the art and include basic salts of a variety of inorganic and organic acids, such as, for example, with inorganic acids, such as for example hydrochloric acid, hydrobromic acid, sulfuric acid or phosphoric acid; with organic carboxylic, sulfonic, sulfo or phospho acids or N-substituted sulfamic acids, for example acetic acid, propionic acid, glycolic acid, succinic acid, maleic acid, hydroxymaleic acid, methylmaleic acid, fumaric acid, malic acid, tartaric acid, lactic acid, oxalic acid, gluconic acid, glucaric acid, glucuronic acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, salicylic acid, 4-aminosalicylic acid, 2-phenoxybenzoic acid, 2-acetoxybenzoic acid, embonic acid, nicotinic acid or isonicotinic acid; and with amino acids, such as the 20 alpha-amino acids involved in the synthesis of proteins in nature, for example glutamic acid or aspartic acid, and also with phenylacetic acid, methanesulfonic acid, ethanesulfonic acid, 2-hydroxyethanesulfonic acid, ethane-1,2-disulfonic acid, benzenesulfonic acid, 4-methylbenzenesulfonic acid, naphthalene-2-sulfonic acid, naphthalene-1,5-disulfonic acid, 2- or 3-phosphoglycerate, glucose-6-phosphate, N-cyclohexylsulfamic acid (with the formation of cyclamates), or with other acid organic compounds, such as ascorbic acid. Pharmaceutically acceptable salts of compounds may also be prepared with a pharmaceutically acceptable cation. Suitable pharmaceutically acceptable cations are well known to those skilled in the art and include alkaline, alkaline earth, ammonium and quaternary ammonium cations. Carbonates or hydrogen carbonates are also possible.

[0062] For oligonucleotides, preferred examples of pharmaceutically acceptable salts include but are not limited to (a) salts formed with cations such as sodium, potassium, ammonium, magnesium, calcium, polyamines such as spermine and spermidine, etc.; (b) acid addition salts formed with inorganic acids, for example hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, nitric acid and the like; (c) salts formed with organic acids such as, for example, acetic acid, oxalic acid, tartaric acid, succinic acid, maleic acid, fumaric acid, gluconic acid, citric acid, malic acid, ascorbic acid, benzoic acid, tannic acid, palmitic acid, alginic acid, polyglutamic acid, naphthalenesulfonic acid, methanesulfonic acid, p-toluenesulfonic acid, naphthalenedisulfonic acid, polygalacturonic acid, and the like; and (d) salts formed from elemental anions such as chlorine, bromine, and iodine.

[0063] The antisense compounds of the present invention can be utilized for diagnostics, therapeutics, prophylaxis and as research reagents and kits. For therapeutics, an animal, preferably a human, suspected of having a disease or disorder which can be treated by modulating the expression of hematopoietic cell protein tyrosine kinase is treated by administering antisense compounds in accordance with this invention. The compounds of the invention can be utilized in pharmaceutical compositions by adding an effective amount of an antisense compound to a suitable pharmaceutically acceptable diluent or carrier. Use of the antisense compounds and methods of the invention may also be useful prophylactically, e.g., to prevent or delay infection, inflammation or tumor formation, for example.

[0064] The antisense compounds of the invention are useful for research and diagnostics, because these compounds hybridize to nucleic acids encoding hematopoietic cell protein tyrosine kinase, enabling sandwich and other assays to easily be constructed to exploit this fact. Hybridization of the antisense oligonucleotides of the invention with a nucleic acid encoding hematopoietic cell protein tyrosine kinase can be detected by means known in the art. Such means may include conjugation of an enzyme to the oligonucleotide, radiolabelling of the oligonucleotide or any other suitable detection means. Kits using such detection means for detecting the level of hematopoietic cell protein tyrosine kinase in a sample may also be prepared.

[0065] The present invention also includes pharmaceutical compositions and formulations which include the antisense compounds of the invention. The pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Oligonucleotides with at least one 2′-O-methoxyethyl modification are believed to be particularly useful for oral administration.

[0066] Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable. Coated condoms, gloves and the like may also be useful. Preferred topical formulations include those in which the oligonucleotides of the invention are in admixture with a topical delivery agent such as lipids, liposomes, fatty acids, fatty acid esters, steroids, chelating agents and surfactants. Preferred lipids and liposomes include neutral (e.g. dioleoylphosphatidyl DOPE ethanolamine, dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline) negative (e.g. dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g. dioleoyltetramethylaminopropyl DOTAP and dioleoylphosphatidyl ethanolamine DOTMA). Oligonucleotides of the invention may be encapsulated within liposomes or may form complexes thereto, in particular to cationic liposomes. Alternatively, oligonucleotides may be complexed to lipids, in particular to cationic lipids. Preferred fatty acids and esters include but are not limited arachidonic acid, oleic acid, eicosanoic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or a C₁₋₁₀ alkyl ester (e.g. isopropylmyristate IPM), monoglyceride, diglyceride or pharmaceutically acceptable salt thereof. Topical formulations are described in detail in U.S. patent application Ser. No. 09/315,298 filed on May 20, 1999 which is incorporated herein by reference in its entirety.

[0067] Compositions and formulations for oral administration include powders or granules, microparticulates, nanoparticulates, suspensions or solutions in water or non-aqueous media, capsules, gel capsules, sachets, tablets or minitablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders may be desirable. Preferred oral formulations are those in which oligonucleotides of the invention are administered in conjunction with one or more penetration enhancers surfactants and chelators. Preferred surfactants include fatty acids and/or esters or salts thereof, bile acids and/or salts thereof. Prefered bile acids/salts include chenodeoxycholic acid (CDCA) and ursodeoxychenodeoxycholic acid (UDCA), cholic acid, dehydrocholic acid, deoxycholic acid, glucholic acid, glycholic acid, glycodeoxycholic acid, taurocholic acid, taurodeoxycholic acid, sodium tauro-24,25-dihydro-fusidate, sodium glycodihydrofusidate. Prefered fatty acids include arachidonic acid, undecanoic acid, oleic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or a monoglyceride, a diglyceride or a pharmaceutically acceptable salt thereof (e.g. sodium). Also prefered are combinations of penetration enhancers, for example, fatty acids/salts in combination with bile acids/salts. A particularly prefered combination is the sodium salt of lauric acid, capric acid and UDCA. Further penetration enhancers include polyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether. Oligonucleotides of the invention may be delivered orally in granular form including sprayed dried particles, or complexed to form micro or nanoparticles. Oligonucleotide complexing agents include poly-amino acids; polyimines; polyacrylates; polyalkylacrylates, polyoxethanes, polyalkylcyanoacrylates; cationized gelatins, albumins, starches, acrylates, polyethyleneglycols (PEG) and starches; polyalkylcyanoacrylates; DEAE-derivatized polyimines, pollulans, celluloses and starches. Particularly preferred complexing agents include chitosan, N-trimethylchitosan, poly-L-lysine, polyhistidine, polyornithine, polyspermines, protamine, polyvinylpyridine, polythiodiethylamino-methylethylene P(TDAE), polyaminostyrene (e.g. p-amino), poly(methylcyanoacrylate), poly(ethylcyanoacrylate), poly(butylcyanoacrylate), poly(isobutylcyanoacrylate), poly(isohexylcynaoacrylate), DEAE-methacrylate, DEAE-hexylacrylate, DEAE-acrylamide, DEAE-albumin and DEAE-dextran, polymethylacrylate, polyhexylacrylate, poly(D, L-lactic acid), poly(DL-lactic-co-glycolic acid (PLGA), alginate, and polyethyleneglycol (PEG). Oral formulations for oligonucleotides and their preparation are described in detail in U.S. applications Ser. No. 08/886,829 (filed Jul. 1, 1997), 09/108,673 (filed Jul. 1, 1998), 09/256,515 (filed Feb. 23, 1999), 09/082,624 (filed May 21, 1998) and Ser. No. 09/315,298 (filed May 20, 1999) each of which is incorporated herein by reference in their entirety.

[0068] Compositions and formulations for parenteral, intrathecal or intraventricular administration may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.

[0069] Pharmaceutical compositions of the present invention include, but are not limited to, solutions, emulsions, and liposome-containing formulations. These compositions may be generated from a variety of components that include, but are not limited to, preformed liquids, self-emulsifying solids and self-emulsifying semisolids.

[0070] The pharmaceutical formulations of the present invention, which may conveniently be presented in unit dosage form, may be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.

[0071] The compositions of the present invention may be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions of the present invention may also be formulated as suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions may further contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension may also contain stabilizers.

[0072] In one embodiment of the present invention the pharmaceutical compositions may be formulated and used as foams. Pharmaceutical foams include formulations such as, but not limited to, emulsions, microemulsions, creams, jellies and liposomes. While basically similar in nature these formulations vary in the components and the consistency of the final product. The preparation of such compositions and formulations is generally known to those skilled in the pharmaceutical and formulation arts and may be applied to the formulation of the compositions of the present invention.

[0073] Emulsions

[0074] The compositions of the present invention may be prepared and formulated as emulsions. Emulsions are typically heterogenous systems of one liquid dispersed in another in the form of droplets usually exceeding 0.1 μm in diameter. (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., Volume 1, p. 245; Block in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 2, p. 335; Higuchi et al., in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 301). Emulsions are often biphasic systems comprising of two immiscible liquid phases intimately mixed and dispersed with each other. In general, emulsions may be either water-in-oil (w/o) or of the oil-in-water (o/w) variety. When an aqueous phase is finely divided into and dispersed as minute droplets into a bulk oily phase the resulting composition is called a water-in-oil (w/o) emulsion. Alternatively, when an oily phase is finely divided into and dispersed as minute droplets into a bulk aqueous phase the resulting composition is called an oil-in-water (o/w) emulsion. Emulsions may contain additional components in addition to the dispersed phases and the active drug which may be present as a solution in either the aqueous phase, oily phase or itself as a separate phase. Pharmaceutical excipients such as emulsifiers, stabilizers, dyes, and anti-oxidants may also be present in emulsions as needed. Pharmaceutical emulsions may also be multiple emulsions that are comprised of more than two phases such as, for example, in the case of oil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions. Such complex formulations often provide certain advantages that simple binary emulsions do not. Multiple emulsions in which individual oil droplets of an o/w emulsion enclose small water droplets constitute a w/o/w emulsion. Likewise a system of oil droplets enclosed in globules of water stabilized in an oily continuous provides an o/w/o emulsion.

[0075] Emulsions are characterized by little or no thermodynamic stability. Often, the dispersed or discontinuous phase of the emulsion is well dispersed into the external or continuous phase and maintained in this form through the means of emulsifiers or the viscosity of the formulation. Either of the phases of the emulsion may be a semisolid or a solid, as is the case of emulsion-style ointment bases and creams. Other means of stabilizing emulsions entail the use of emulsifiers that may be incorporated into either phase of the emulsion. Emulsifiers may broadly be classified into four categories: synthetic surfactants, naturally occurring emulsifiers, absorption bases, and finely dispersed solids (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

[0076] Synthetic surfactants, also known as surface active agents, have found wide applicability in the formulation of emulsions and have been reviewed in the literature (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199). Surfactants are typically amphiphilic and comprise a hydrophilic and a hydrophobic portion. The ratio of the hydrophilic to the hydrophobic nature of the surfactant has been termed the hydrophile/lipophile balance (HLB) and is a valuable tool in categorizing and selecting surfactants in the preparation of formulations. Surfactants may be classified into different classes based on the nature of the hydrophilic group: nonionic, anionic, cationic and amphoteric (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285).

[0077] Naturally occurring emulsifiers used in emulsion formulations include lanolin, beeswax, phosphatides, lecithin and acacia. Absorption bases possess hydrophilic properties such that they can soak up water to form w/o emulsions yet retain their semisolid consistencies, such as anhydrous lanolin and hydrophilic petrolatum. Finely divided solids have also been used as good emulsifiers especially in combination with surfactants and in viscous preparations. These include polar inorganic solids, such as heavy metal hydroxides, nonswelling clays such as bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal magnesium aluminum silicate, pigments and nonpolar solids such as carbon or glyceryl tristearate.

[0078] A large variety of non-emulsifying materials are also included in emulsion formulations and contribute to the properties of emulsions. These include fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives and antioxidants (Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

[0079] Hydrophilic colloids or hydrocolloids include naturally occurring gums and synthetic polymers such as polysaccharides (for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth), cellulose derivatives (for example, carboxymethylcellulose and carboxypropylcellulose), and synthetic polymers (for example, carbomers, cellulose ethers, and carboxyvinyl polymers). These disperse or swell in water to form colloidal solutions that stabilize emulsions by forming strong interfacial films around the dispersed-phase droplets and by increasing the viscosity of the external phase.

[0080] Since emulsions often contain a number of ingredients such as carbohydrates, proteins, sterols and phosphatides that may readily support the growth of microbes, these formulations often incorporate preservatives. Commonly used preservatives included in emulsion formulations include methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid. Antioxidants are also commonly added to emulsion formulations to prevent deterioration of the formulation. Antioxidants used may be free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulfite, and antioxidant synergists such as citric acid, tartaric acid, and lecithin.

[0081] The application of emulsion formulations via dermatological, oral and parenteral routes and methods for their manufacture have been reviewed in the literature (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Emulsion formulations for oral delivery have been very widely used because of reasons of ease of formulation, efficacy from an absorption and bioavailability standpoint. (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Mineral-oil base laxatives, oil-soluble vitamins and high fat nutritive preparations are among the materials that have commonly been administered orally as o/w emulsions.

[0082] In one embodiment of the present invention, the compositions of oligonucleotides and nucleic acids are formulated as microemulsions. A microemulsion may be defined as a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Typically microemulsions are systems that are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a fourth component, generally an intermediate chain-length alcohol to form a transparent system. Therefore, microemulsions have also been described as thermodynamically stable, isotropically clear dispersions of two immiscible liquids that are stabilized by interfacial films of surface-active molecules (Leung and Shah, in: Controlled Release of Drugs: Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH Publishers, New York, pages 185-215). Microemulsions commonly are prepared via a combination of three to five components that include oil, water, surfactant, cosurfactant and electrolyte. Whether the microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w) type is dependent on the properties of the oil and surfactant used and on the structure and geometric packing of the polar heads and hydrocarbon tails of the surfactant molecules (Schott, in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 271).

[0083] The phenomenological approach utilizing phase diagrams has been extensively studied and has yielded a comprehensive knowledge, to one skilled in the art, of how to formulate microemulsions (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335). Compared to conventional emulsions, microemulsions offer the advantage of solubilizing water-insoluble drugs in a formulation of thermodynamically stable droplets that are formed spontaneously.

[0084] Surfactants used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750), decaglycerol decaoleate (DAO750), alone or in combination with cosurfactants. The cosurfactant, usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules. Microemulsions may, however, be prepared without the use of cosurfactants and alcohol-free self-emulsifying microemulsion systems are known in the art. The aqueous phase may typically be, but is not limited to, water, an aqueous solution of the drug, glycerol, PEG300, PEG400, polyglycerols, propylene glycols, and derivatives of ethylene glycol. The oil phase may include, but is not limited to, materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.

[0085] Microemulsions are particularly of interest from the standpoint of drug solubilization and the enhanced absorption of drugs. Lipid based microemulsions (both o/w and w/o) have been proposed to enhance the oral bioavailability of drugs, including peptides (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385-1390; Ritschel, Meth. Find. Exp. Clin. Pharmacol., 1993, 13, 205). Microemulsions afford advantages of improved drug solubilization, protection of drug from enzymatic hydrolysis, possible enhancement of drug absorption due to surfactant-induced alterations in membrane fluidity and permeability, ease of preparation, ease of oral administration over solid dosage forms, improved clinical potency, and decreased toxicity (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J. Pharm. Sci., 1996, 85, 138-143). Often microemulsions may form spontaneously when their components are brought together at ambient temperature. This may be particularly advantageous when formulating thermolabile drugs, peptides or oligonucleotides. Microemulsions have also been effective in the transdermal delivery of active components in both cosmetic and pharmaceutical applications. It is expected that the microemulsion compositions and formulations of the present invention will facilitate the increased systemic absorption of oligonucleotides and nucleic acids from the gastrointestinal tract, as well as improve the local cellular uptake of oligonucleotides and nucleic acids within the gastrointestinal tract, vagina, buccal cavity and other areas of administration.

[0086] Microemulsions of the present invention may also contain additional components and additives such as sorbitan monostearate (Grill 3), Labrasol, and penetration enhancers to improve the properties of the formulation and to enhance the absorption of the oligonucleotides and nucleic acids of the present invention. Penetration enhancers used in the microemulsions of the present invention may be classified as belonging to one of five broad categories—surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of these classes has been discussed above.

[0087] Liposomes

[0088] There are many organized surfactant structures besides microemulsions that have been studied and used for the formulation of drugs. These include monolayers, micelles, bilayers and vesicles. Vesicles, such as liposomes, have attracted great interest because of their specificity and the duration of action they offer from the standpoint of drug delivery. As used in the present invention, the term “liposome” means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers.

[0089] Liposomes are unilamellar or multilamellar vesicles which have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the composition to be delivered. Cationic liposomes possess the advantage of being able to fuse to the cell wall. Non-cationic liposomes, although not able to fuse as efficiently with the cell wall, are taken up by macrophages in vivo.

[0090] In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient. Therefore, it is desirable to use a liposome which is highly deformable and able to pass through such fine pores.

[0091] Further advantages of liposomes include; liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect encapsulated drugs in their internal compartments from metabolism and degradation (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.

[0092] Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomes start to merge with the cellular membranes. As the merging of the liposome and cell progresses, the liposomal contents are emptied into the cell where the active agent may act.

[0093] Liposomal formulations have been the focus of extensive investigation as the mode of delivery for many drugs. There is growing evidence that for topical administration, liposomes present several advantages over other formulations. Such advantages include reduced side-effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at the desired target, and the ability to administer a wide variety of drugs, both hydrophilic and hydrophobic, into the skin.

[0094] Several reports have detailed the ability of liposomes to deliver agents including high-molecular weight DNA into the skin. Compounds including analgesics, antibodies, hormones and high-molecular weight DNAs have been administered to the skin. The majority of applications resulted in the targeting of the upper epidermis.

[0095] Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes which interact with the negatively charged DNA molecules to form a stable complex. The positively charged DNA/liposome complex binds to the negatively charged cell surface and is internalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm (Wang et al., Biochem. Biophys. Res. Commun., 1987, 147, 980-985).

[0096] Liposomes which are pH-sensitive or negatively-charged, entrap DNA rather than complex with it. Since both the DNA and the lipid are similarly charged, repulsion rather than complex formation occurs. Nevertheless, some DNA is entrapped within the aqueous interior of these liposomes. pH-sensitive liposomes have been used to deliver DNA encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 1992, 19, 269-274).

[0097] One major type of liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine. Neutral liposome compositions, for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC). Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC. Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.

[0098] Several studies have assessed the topical delivery of liposomal drug formulations to the skin. Application of liposomes containing interferon to guinea pig skin resulted in a reduction of skin herpes sores while delivery of interferon via other means (e.g. as a solution or as an emulsion) were ineffective (Weiner et al., Journal of Drug Targeting, 1992, 2, 405-410). Further, an additional study tested the efficacy of interferon administered as part of a liposomal formulation to the administration of interferon using an aqueous system, and concluded that the liposomal formulation was superior to aqueous administration (du Plessis et al., Antiviral Research, 1992, 18, 259-265).

[0099] Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol. Non-ionic liposomal formulations comprising Novasome™ (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome™ II (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver cyclosporin-A into the dermis of mouse skin. Results indicated that such non-ionic liposomal systems were effective in facilitating the deposition of cyclosporin-A into different layers of the skin (Hu et al. S.T.P. Pharma. Sci., 1994, 4, 6, 466).

[0100] Liposomes also include “sterically stabilized” liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids that, when incorporated into liposomes, result in enhanced circulation lifetimes relative to liposomes lacking such specialized lipids. Examples of sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome (A) comprises one or more glycolipids, such as monosialoganglioside G_(M1), or (B) is derivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety. While not wishing to be bound by any particular theory, it is thought in the art that, at least for sterically stabilized liposomes containing gangliosides, sphingomyelin, or PEG-derivatized lipids, the enhanced circulation half-life of these sterically stabilized liposomes derives from a reduced uptake into cells of the reticuloendothelial system (RES) (Allen et al., FEBS Letters, 1987, 223, 42; Wu et al., Cancer Research, 1993, 53, 3765).

[0101] Various liposomes comprising one or more glycolipids are known in the art. Papahadjopoulos et al. (Ann. N.Y. Acad. Sci., 1987, 507, 64) reported the ability of monosialoganglioside G_(M1), galactocerebroside sulfate and phosphatidylinositol to improve blood half-lives of liposomes. These findings were expounded upon by Gabizon et al. (Proc. Natl. Acad. Sci. U.S.A., 1988, 85, 6949). U.S. Pat. No. 4,837,028 and WO 88/04924, both to Allen et al., disclose liposomes comprising (1) sphingomyelin and (2) the ganglioside G_(M1) or a galactocerebroside sulfate ester. U.S. Pat. No. 5,543,152 (Webb et al.) discloses liposomes comprising sphingomyelin. Liposomes comprising 1,2-sn-dimyristoylphosphatidylcholine are disclosed in WO 97/13499 (Lim et al.).

[0102] Many liposomes comprising lipids derivatized with one or more hydrophilic polymers, and methods of preparation thereof, are known in the art. Sunamoto et al. (Bull. Chem. Soc. Jpn., 1980, 53, 2778) described liposomes comprising a nonionic detergent, 2C₁₂15G, that contains a PEG moiety. Illum et al. (FEBS Lett., 1984, 167, 79) noted that hydrophilic coating of polystyrene particles with polymeric glycols results in significantly enhanced blood half-lives. Synthetic phospholipids modified by the attachment of carboxylic groups of polyalkylene glycols (e.g., PEG) are described by Sears (U.S. Pat. Nos. 4,426,330 and 4,534,899). Klibanov et al. (FEBS Lett., 1990, 268, 235) described experiments demonstrating that liposomes comprising phosphatidylethanolamine (PE) derivatized with PEG or PEG stearate have significant increases in blood circulation half-lives. Blume et al. (Biochimica et Biophysica Acta, 1990, 1029, 91) extended such observations to other PEG-derivatized phospholipids, e.g., DSPE-PEG, formed from the combination of distearoylphosphatidylethanolamine (DSPE) and PEG. Liposomes having covalently bound PEG moieties on their external surface are described in European Patent No. EP 0 445 131 B1 and WO 90/04384 to Fisher. Liposome compositions containing 1-20 mole percent of PE derivatized with PEG, and methods of use thereof, are described by Woodle et al. (U.S. Pat. Nos. 5,013,556 and 5,356,633) and Martin et al. (U.S. Pat. No. 5,213,804 and European Patent No. EP 0 496 813 B1). Liposomes comprising a number of other lipid-polymer conjugates are disclosed in WO 91/05545 and U.S. Pat. No. 5,225,212 (both to Martin et al.) and in WO 94/20073 (Zalipsky et al.) Liposomes comprising PEG-modified ceramide lipids are described in WO 96/10391 (Choi et al.). U.S. Pat. Nos. 5,540,935 (Miyazaki et al.) and 5,556,948 (Tagawa et al.) describe PEG-containing liposomes that can be further derivatized with functional moieties on their surfaces.

[0103] A limited number of liposomes comprising nucleic acids are known in the art. WO 96/40062 to Thierry et al. discloses methods for encapsulating high molecular weight nucleic acids in liposomes. U.S. Pat. No. 5,264,221 to Tagawa et al. discloses protein-bonded liposomes and asserts that the contents of such liposomes may include an antisense RNA. U.S. Pat. No. 5,665,710 to Rahman et al. describes certain methods of encapsulating oligodeoxynucleotides in liposomes. WO 97/04787 to Love et al. discloses liposomes comprising antisense oligonucleotides targeted to the raf gene.

[0104] Transfersomes are yet another type of liposomes, and are highly deformable lipid aggregates which are attractive candidates for drug delivery vehicles. Transfersomes may be described as lipid droplets which are so highly deformable that they are easily able to penetrate through pores which are smaller than the droplet. Transfersomes are adaptable to the environment in which they are used, e.g. they are self-optimizing (adaptive to the shape of pores in the skin), self-repairing, frequently reach their targets without fragmenting, and often self-loading. To make transfersomes it is possible to add surface edge-activators, usually surfactants, to a standard liposomal composition. Transfersomes have been used to deliver serum albumin to the skin. The transfersome-mediated delivery of serum albumin has been shown to be as effective as subcutaneous injection of a solution containing serum albumin.

[0105] Surfactants find wide application in formulations such as emulsions (including microemulsions) and liposomes. The most common way of classifying and ranking the properties of the many different types of surfactants, both natural and synthetic, is by the use of the hydrophile/lipophile balance (HLB). The nature of the hydrophilic group (also known as the “head”) provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

[0106] If the surfactant molecule is not ionized, it is classified as a nonionic surfactant. Nonionic surfactants find wide application in pharmaceutical and cosmetic products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure. Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class. The polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.

[0107] If the surfactant molecule carries a negative charge when it is dissolved or dispersed in water, the surfactant is classified as anionic. Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates. The most important members of the anionic surfactant class are the alkyl sulfates and the soaps.

[0108] If the surfactant molecule carries a positive charge when it is dissolved or dispersed in water, the surfactant is classified as cationic. Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.

[0109] If the surfactant molecule has the ability to carry either a positive or negative charge, the surfactant is classified as amphoteric. Amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.

[0110] The use of surfactants in drug products, formulations and in emulsions has been reviewed (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

[0111] Penetration Enhancers

[0112] In one embodiment, the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly oligonucleotides, to the skin of animals. Most drugs are present in solution in both ionized and nonionized forms. However, usually only lipid soluble or lipophilic drugs readily cross cell membranes. It has been discovered that even non-lipophilic drugs may cross cell membranes if the membrane to be crossed is treated with a penetration enhancer. In addition to aiding the diffusion of non-lipophilic drugs across cell membranes, penetration enhancers also enhance the permeability of lipophilic drugs.

[0113] Penetration enhancers may be classified as belonging to one of five broad categories, i.e., surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92). Each of the above mentioned classes of penetration enhancers are described below in greater detail.

[0114] Surfactants: In connection with the present invention, surfactants (or “surface-active agents”) are chemical entities which, when dissolved in an aqueous solution, reduce the surface tension of the solution or the interfacial tension between the aqueous solution and another liquid, with the result that absorption of oligonucleotides through the mucosa is enhanced. In addition to bile salts and fatty acids, these penetration enhancers include, for example, sodium lauryl sulfate, polyoxyethylene-9-lauryl ether and polyoxyethylene-20-cetyl ether) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92); and perfluorochemical emulsions, such as FC-43. Takahashi et al., J. Pharm. Pharmacol., 1988, 40, 252).

[0115] Fatty acids: Various fatty acids and their derivatives which act as penetration enhancers include, for example, oleic acid, lauric acid, capric acid (n-decanoic acid), myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein (1-monooleoyl-rac-glycerol), dilaurin, caprylic acid, arachidonic acid, glycerol 1-monocaprate, 1-dodecylazacycloheptan-2-one, acylcarnitines, acylcholines, C₁₋₁₀ alkyl esters thereof (e.g., methyl, isopropyl and t-butyl), and mono- and di-glycerides thereof (i.e., oleate, laurate, caprate, myristate, palmitate, stearate, linoleate, etc.) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; El Hariri et al., J. Pharm. Pharmacol., 1992, 44, 651-654).

[0116] Bile salts: The physiological role of bile includes the facilitation of dispersion and absorption of lipids and fat-soluble vitamins (Brunton, Chapter 38 in: Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9th Ed., Hardman et al. Eds., McGraw-Hill, New York, 1996, pp. 934-935). Various natural bile salts, and their synthetic derivatives, act as penetration enhancers. Thus the term “bile salts” includes any of the naturally occurring components of bile as well as any of their synthetic derivatives. The bile salts of the invention include, for example, cholic acid (or its pharmaceutically acceptable sodium salt, sodium cholate), dehydrocholic acid (sodium dehydrocholate), deoxycholic acid (sodium deoxycholate), glucholic acid (sodium glucholate), glycholic acid (sodium glycocholate), glycodeoxycholic acid (sodium glycodeoxycholate), taurocholic acid (sodium taurocholate), taurodeoxycholic acid (sodium taurodeoxycholate), chenodeoxycholic acid (sodium chenodeoxycholate), ursodeoxycholic acid (UDCA), sodium tauro-24,25-dihydro-fusidate (STDHF), sodium glycodihydrofusidate and polyoxyethylene-9-lauryl ether (POE) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Swinyard, Chapter 39 In: Remington's Pharmaceutical Sciences, 18th Ed., Gennaro, ed., Mack Publishing Co., Easton, Pa., 1990, pages 782-783; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Yamamoto et al., J. Pharm. Exp. Ther., 1992, 263, 25; Yamashita et al., J. Pharm. Sci., 1990, 79, 579-583).

[0117] Chelating Agents: Chelating agents, as used in connection with the present invention, can be defined as compounds that remove metallic ions from solution by forming complexes therewith, with the result that absorption of oligonucleotides through the mucosa is enhanced. With regards to their use as penetration enhancers in the present invention, chelating agents have the added advantage of also serving as DNase inhibitors, as most characterized DNA nucleases require a divalent metal ion for catalysis and are thus inhibited by chelating agents (Jarrett, J. Chromatogr., 1993, 618, 315-339). Chelating agents of the invention include but are not limited to disodium ethylenediaminetetraacetate (EDTA), citric acid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate and homovanilate), N-acyl derivatives of collagen, laureth-9 and N-amino acyl derivatives of beta-diketones (enamines)(Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Buur et al., J. Control Rel., 1990, 14, 43-51).

[0118] Non-chelating non-surfactants: As used herein, non-chelating non-surfactant penetration enhancing compounds can be defined as compounds that demonstrate insignificant activity as chelating agents or as surfactants but that nonetheless enhance absorption of oligonucleotides through the alimentary mucosa (Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33). This class of penetration enhancers include, for example, unsaturated cyclic ureas, 1-alkyl- and 1-alkenylazacyclo-alkanone derivatives (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92); and non steroidal anti-inflammatory agents such as diclofenac sodium, indomethacin and phenylbutazone (Yamashita et al., J. Pharm. Pharmacol., 1987, 39, 621-626).

[0119] Agents that enhance uptake of oligonucleotides at the cellular level may also be added to the pharmaceutical and other compositions of the present invention. For example, cationic lipids, such as lipofectin (Junichi et al, U.S. Pat. No. 5,705,188), cationic glycerol derivatives, and polycationic molecules, such as polylysine (Lollo et al., PCT Application WO 97/30731), are also known to enhance the cellular uptake of oligonucleotides.

[0120] Other agents may be utilized to enhance the penetration of the administered nucleic acids, including glycols such as ethylene glycol and propylene glycol, pyrrols such as 2-pyrrol, azones, and terpenes such as limonene and menthone.

[0121] Carriers

[0122] Certain compositions of the present invention also incorporate carrier compounds in the formulation. As used herein, “carrier compound” or “carrier” can refer to a nucleic acid, or analog thereof, which is inert (i.e., does not possess biological activity per se) but is recognized as a nucleic acid by in vivo processes that reduce the bioavailability of a nucleic acid having biological activity by, for example, degrading the biologically active nucleic acid or promoting its removal from circulation. The coadministration of a nucleic acid and a carrier compound, typically with an excess of the latter substance, can result in a substantial reduction of the amount of nucleic acid recovered in the liver, kidney or other extracirculatory reservoirs, presumably due to competition between the carrier compound and the nucleic acid for a common receptor. For example, the recovery of a partially phosphorothioate oligonucleotide in hepatic tissue can be reduced when it is coadministered with polyinosinic acid, dextran sulfate, polycytidic acid or 4-acetamido-4′isothiocyano-stilbene-2,2′-disulfonic acid (Miyao et al., Antisense Res. Dev., 1995, 5, 115-121; Takakura et al., Antisense & Nucl. Acid Drug Dev., 1996, 6, 177-183).

[0123] Excipients

[0124] In contrast to a carrier compound, a “pharmaceutical carrier” or “excipient” is a pharmaceutically acceptable solvent, suspending agent or any other pharmacologically inert vehicle for delivering one or more nucleic acids to an animal. The excipient may be liquid or solid and is selected, with the planned manner of administration in mind, so as to provide for the desired bulk, consistency, etc., when combined with a nucleic acid and the other components of a given pharmaceutical composition. Typical pharmaceutical carriers include, but are not limited to, binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and other sugars, microcrystalline cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates or calcium hydrogen phosphate, etc.); lubricants (e.g., magnesium stearate, talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates, hydrogenated vegetable oils, corn starch, polyethylene glycols, sodium benzoate, sodium acetate, etc.); disintegrants (e.g., starch, sodium starch glycolate, etc.); and wetting agents (e.g., sodium lauryl sulphate, etc.).

[0125] Pharmaceutically acceptable organic or inorganic excipient suitable for non-parenteral administration which do not deleteriously react with nucleic acids can also be used to formulate the compositions of the present invention. Suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

[0126] Formulations for topical administration of nucleic acids may include sterile and non-sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions of the nucleic acids in liquid or solid oil bases. The solutions may also contain buffers, diluents and other suitable additives. Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can be used.

[0127] Suitable pharmaceutically acceptable excipients include, but are not limited to, water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

[0128] Other Components

[0129] The compositions of the present invention may additionally contain other adjunct components conventionally found in pharmaceutical compositions, at their art-established usage levels. Thus, for example, the compositions may contain additional, compatible, pharmaceutically-active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or may contain additional materials useful in physically formulating various dosage forms of the compositions of the present invention, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. However, such materials, when added, should not unduly interfere with the biological activities of the components of the compositions of the present invention. The formulations can be sterilized and, if desired, mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously interact with the nucleic acid(s) of the formulation.

[0130] Aqueous suspensions may contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension may also contain stabilizers.

[0131] Certain embodiments of the invention provide pharmaceutical compositions containing (a) one or more antisense compounds and (b) one or more other chemotherapeutic agents which function by a non-antisense mechanism. Examples of such chemotherapeutic agents include but are not limited to daunorubicin, daunomycin, dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin, bleomycin, mafosfamide, ifosfamide, cytosine arabinoside, bis-chloroethylnitrosurea, busulfan, mitomycin C, actinomycin D, mithramycin, prednisone, hydroxyprogesterone, testosterone, tamoxifen, dacarbazine, procarbazine, hexamethylmelamine, pentamethylmelamine, mitoxantrone, amsacrine, chlorambucil, methylcyclohexylnitrosurea, nitrogen mustards, melphalan, cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-azacytidine, hydroxyurea, deoxycoformycin, 4-hydroxyperoxycyclophosphoramide, 5-fluorouracil (5-FU), 5-fluorodeoxyuridine (5-FUdR), methotrexate (MTX), colchicine, taxol, vincristine, vinblastine, etoposide (VP-16), trimetrexate, irinotecan, topotecan, gemcitabine, teniposide, cisplatin and diethylstilbestrol (DES). See, generally, The Merck Manual of Diagnosis and Therapy, 15th Ed. 1987, pp. 1206-1228, Berkow et al., eds., Rahway, N.J. When used with the compounds of the invention, such chemotherapeutic agents may be used individually (e.g., 5-FU and oligonucleotide), sequentially (e.g., 5-FU and oligonucleotide for a period of time followed by MTX and oligonucleotide), or in combination with one or more other such chemotherapeutic agents (e.g., 5-FU, MTX and oligonucleotide, or 5-FU, radiotherapy and oligonucleotide). Anti-inflammatory drugs, including but not limited to nonsteroidal anti-inflammatory drugs and corticosteroids, and antiviral drugs, including but not limited to ribivirin, vidarabine, acyclovir and ganciclovir, may also be combined in compositions of the invention. See, generally, The Merck Manual of Diagnosis and Therapy, 15th Ed., Berkow et al., eds., 1987, Rahway, N.J., pages 2499-2506 and 46-49, respectively). Other non-antisense chemotherapeutic agents are also within the scope of this invention. Two or more combined compounds may be used together or sequentially.

[0132] In another related embodiment, compositions of the invention may contain one or more antisense compounds, particularly oligonucleotides, targeted to a first nucleic acid and one or more additional antisense compounds targeted to a second nucleic acid target. Numerous examples of antisense compounds are known in the art. Two or more combined compounds may be used together or sequentially.

[0133] The formulation of therapeutic compositions and their subsequent administration is believed to be within the skill of those in the art. Dosing is dependent on severity and responsiveness of the disease state to be treated, with the course of treatment lasting from several days to several months, or until a cure is effected or a diminution of the disease state is achieved. Optimal dosing schedules can be calculated from measurements of drug accumulation in the body of the patient. Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates. Optimum dosages may vary depending on the relative potency of individual oligonucleotides, and can generally be estimated based on EC₅₀s found to be effective in in vitro and in vivo animal models. In general, dosage is from 0.01 ug to 100 g per kg of body weight, and may be given once or more daily, weekly, monthly or yearly, or even once every 2 to 20 years. Persons of ordinary skill in the art can easily estimate repetition rates for dosing based on measured residence times and concentrations of the drug in bodily fluids or tissues. Following successful treatment, it may be desirable to have the patient undergo maintenance therapy to prevent the recurrence of the disease state, wherein the oligonucleotide is administered in maintenance doses, ranging from 0.01 ug to 100 g per kg of body weight, once or more daily, to once every 20 years.

[0134] While the present invention has been described with specificity in accordance with certain of its preferred embodiments, the following examples serve only to illustrate the invention and are not intended to limit the same.

EXAMPLES Example 1

[0135] Nucleoside Phosphoramidites for Oligonucleotide Synthesis Deoxy and 2′-alkoxy Amidites

[0136] 2′-Deoxy and 2′-methoxy beta-cyanoethyldiisopropyl phosphoramidites were purchased from commercial sources (e.g. Chemgenes, Needham Mass. or Glen Research, Inc. Sterling Va.). Other 2′-O-alkoxy substituted nucleoside amidites are prepared as described in U.S. Pat. No. 5,506,351, herein incorporated by reference. For oligonucleotides synthesized using 2′-alkoxy amidites, the standard cycle for unmodified oligonucleotides was utilized, except the wait step after pulse delivery of tetrazole and base was increased to 360 seconds.

[0137] Oligonucleotides containing 5-methyl-2′-deoxycytidine (5-Me-C) nucleotides were synthesized according to published methods [Sanghvi, et. al., Nucleic Acids Research, 1993, 21, 3197-3203] using commercially available phosphoramidites (Glen Research, Sterling Va. or ChemGenes, Needham Mass.).

[0138] 2′-Fluoro Amidites

[0139] 2′-Fluorodeoxyadenosine Amidites

[0140] 2′-fluoro oligonucleotides were synthesized as described previously [Kawasaki, et. al., J. Med. Chem., 1993, 36, 831-841] and U.S. Pat. No. 5,670,633, herein incorporated by reference. Briefly, the protected nucleoside N6-benzoyl-2′-deoxy-2′-fluoroadenosine was synthesized utilizing commercially available 9-beta-D-arabinofuranosyladenine as starting material and by modifying literature procedures whereby the 2′-alpha-fluoro atom is introduced by a S_(N)2-displacement of a 2′-beta-trityl group. Thus N6-benzoyl-9-beta-D-arabinofuranosyladenine was selectively protected in moderate yield as the 3′,5′-ditetrahydropyranyl (THP) intermediate. Deprotection of the THP and N6-benzoyl groups was accomplished using standard methodologies and standard methods were used to obtain the 5′-dimethoxytrityl-(DMT) and 5′-DMT-3′-phosphoramidite intermediates.

[0141] 2′-Fluorodeoxyguanosine

[0142] The synthesis of 2′-deoxy-2′-fluoroguanosine was accomplished using tetraisopropyldisiloxanyl (TPDS) protected 9-beta-D-arabinofuranosylguanine as starting material, and conversion to the intermediate diisobutyryl-arabinofuranosylguanosine. Deprotection of the TPDS group was followed by protection of the hydroxyl group with THP to give diisobutyryl di-THP protected arabinofuranosylguanine. Selective O-deacylation and triflation was followed by treatment of the crude product with fluoride, then deprotection of the THP groups. Standard methodologies were used to obtain the 5′-DMT- and 5′-DMT-3′-phosphoramidites.

[0143] 2′-Fluorouridine

[0144] Synthesis of 2′-deoxy-2′-fluorouridine was accomplished by the modification of a literature procedure in which 2,2′-anhydro-1-beta-D-arabinofuranosyluracil was treated with 70% hydrogen fluoride-pyridine. Standard procedures were used to obtain the 5′-DMT and 5′-DMT-3′phosphoramidites.

[0145] 2′-Fluorodeoxycytidine

[0146] 2′-deoxy-2′-fluorocytidine was synthesized via amination of 2′-deoxy-2′-fluorouridine, followed by selective protection to give N4-benzoyl-2′-deoxy-2′-fluorocytidine. Standard procedures were used to obtain the 5′-DMT and 5′-DMT-3′phosphoramidites.

[0147] 2′-O-(2-Methoxyethyl) Modified Amidites

[0148] 2′-O-Methoxyethyl-substituted nucleoside amidites are prepared as follows, or alternatively, as per the methods of Martin, P., Helvetica Chimica Acta, 1995, 78, 486-504.

[0149] 2,2′-Anhydro[1-(beta-D-arabinofuranosyl)-5-methyluridine]

[0150] 5-Methyluridine (ribosylthymine, commercially available through Yamasa, Choshi, Japan) (72.0 g, 0.279 M), diphenyl-carbonate (90.0 g, 0.420 M) and sodium bicarbonate (2.0 g, 0.024 M) were added to DMF (300 mL). The mixture was heated to reflux, with stirring, allowing the evolved carbon dioxide gas to be released in a controlled manner. After 1 hour, the slightly darkened solution was concentrated under reduced pressure. The resulting syrup was poured into diethylether (2.5 L), with stirring. The product formed a gum. The ether was decanted and the residue was dissolved in a minimum amount of methanol (ca. 400 mL). The solution was poured into fresh ether (2.5 L) to yield a stiff gum. The ether was decanted and the gum was dried in a vacuum oven (60° C. at 1 mm Hg for 24 h) to give a solid that was crushed to a light tan powder (57 g, 85% crude yield). The NMR spectrum was consistent with the structure, contaminated with phenol as its sodium salt (ca. 5%). The material was used as is for further reactions (or it can be purified further by column chromatography using a gradient of methanol in ethyl acetate (10-25%) to give a white solid, mp 222-4° C.).

[0151] 2′-O-Methoxyethyl-5-methyluridine

[0152] 2,2′-Anhydro-5-methyluridine (195 g, 0.81 M), tris(2-methoxyethyl)borate (231 g, 0.98 M) and 2-methoxyethanol (1.2 L) were added to a 2 L stainless steel pressure vessel and placed in a pre-heated oil bath at 160° C. After heating for 48 hours at 155-160° C., the vessel was opened and the solution evaporated to dryness and triturated with MeOH (200 mL). The residue was suspended in hot acetone (1 L). The insoluble salts were filtered, washed with acetone (150 mL) and the filtrate evaporated. The residue (280 g) was dissolved in CH₃CN (600 mL) and evaporated. A silica gel column (3 kg) was packed in CH₂Cl₂/acetone/MeOH (20:5:3) containing 0.5% Et₃NH. The residue was dissolved in CH₂Cl₂ (250 mL) and adsorbed onto silica (150 g) prior to loading onto the column. The product was eluted with the packing solvent to give 160 g (63%) of product. Additional material was obtained by reworking impure fractions.

[0153] 2′-O-Methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine

[0154] 2′-O-Methoxyethyl-5-methyluridine (160 g, 0.506 M) was co-evaporated with pyridine (250 mL) and the dried residue dissolved in pyridine (1.3 L). A first aliquot of dimethoxytrityl chloride (94.3 g, 0.278 M) was added and the mixture stirred at room temperature for one hour. A second aliquot of dimethoxytrityl chloride (94.3 g, 0.278 M) was added and the reaction stirred for an additional one hour. Methanol (170 mL) was then added to stop the reaction. HPLC showed the presence of approximately 70% product. The solvent was evaporated and triturated with CH₃CN (200 mL). The residue was dissolved in CHCl₃ (1.5 L) and extracted with 2×500 mL of saturated NaHCO₃ and 2×500 mL of saturated NaCl. The organic phase was dried over Na₂SO₄, filtered and evaporated. 275 g of residue was obtained. The residue was purified on a 3.5 kg silica gel column, packed and eluted with EtOAc/hexane/acetone (5:5:1) containing 0.5% Et₃NH. The pure fractions were evaporated to give 164 g of product. Approximately 20 g additional was obtained from the impure fractions to give a total yield of 183 g (57%).

[0155] 3′-O-Acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine

[0156] 2′-O-Methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine (106 g, 0.167 M), DMF/pyridine (750 mL of a 3:1 mixture prepared from 562 mL of DMF and 188 mL of pyridine) and acetic anhydride (24.38 mL, 0.258 M) were combined and stirred at room temperature for 24 hours. The reaction was monitored by TLC by first quenching the TLC sample with the addition of MeOH. Upon completion of the reaction, as judged by TLC, MeOH (50 mL) was added and the mixture evaporated at 35° C. The residue was dissolved in CHCl₃ (800 mL) and extracted with 2×200 mL of saturated sodium bicarbonate and 2×200 mL of saturated NaCl. The water layers were back extracted with 200 mL of CHCl₃. The combined organics were dried with sodium sulfate and evaporated to give 122 g of residue (approx. 90% product). The residue was purified on a 3.5 kg silica gel column and eluted using EtOAc/hexane (4:1). Pure product fractions were evaporated to yield 96 g (84%). An additional 1.5 g was recovered from later fractions.

[0157] 3′-O-Acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyl-4-triazoleuridine

[0158] A first solution was prepared by dissolving 3′-O-acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine (96 g, 0.144 M) in CH₃CN (700 mL) and set aside. Triethylamine (189 mL, 1.44 M) was added to a solution of triazole (90 g, 1.3 M) in CH₃CN (1 L), cooled to −5° C. and stirred for 0.5 h using an overhead stirrer. POCl₃ was added dropwise, over a 30 minute period, to the stirred solution maintained at 0-10° C., and the resulting mixture stirred for an additional 2 hours. The first solution was added dropwise, over a 45 minute period, to the latter solution. The resulting reaction mixture was stored overnight in a cold room. Salts were filtered from the reaction mixture and the solution was evaporated. The residue was dissolved in EtOAc (1 L) and the insoluble solids were removed by filtration. The filtrate was washed with 1×300 mL of NaHCO₃ and 2×300 mL of saturated NaCl, dried over sodium sulfate and evaporated. The residue was triturated with EtOAc to give the title compound.

[0159] 2′-O-Methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine

[0160] A solution of 3′-O-acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyl-4-triazoleuridine (103 g, 0.141 M) in dioxane (500 mL) and NH₄OH (30 mL) was stirred at room temperature for 2 hours. The dioxane solution was evaporated and the residue azeotroped with MeOH (2×200 mL). The residue was dissolved in MeOH (300 mL) and transferred to a 2 liter stainless steel pressure vessel. MeOH (400 mL) saturated with NH₃ gas was added and the vessel heated to 100° C. for 2 hours (TLC showed complete conversion). The vessel contents were evaporated to dryness and the residue was dissolved in EtOAc (500 mL) and washed once with saturated NaCl (200 mL). The organics were dried over sodium sulfate and the solvent was evaporated to give 85 g (95%) of the title compound.

[0161] N4-Benzoyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine

[0162] 2′-O-Methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine (85 g, 0.134 M) was dissolved in DMF (800 mL) and benzoic anhydride (37.2 g, 0.165 M) was added with stirring. After stirring for 3 hours, TLC showed the reaction to be approximately 95% complete. The solvent was evaporated and the residue azeotroped with MeOH (200 mL). The residue was dissolved in CHCl₃ (700 mL) and extracted with saturated NaHCO₃ (2×300 mL) and saturated NaCl (2×300 mL), dried over MgSO₄ and evaporated to give a residue (96 g). The residue was chromatographed on a 1.5 kg silica column using EtOAc/hexane (1:1) containing 0.5% Et₃NH as the eluting solvent. The pure product fractions were evaporated to give 90 g (90%) of the title compound.

[0163] N4-Benzoyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine-3′-amidite

[0164] N4-Benzoyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine (74 g, 0.10 M) was dissolved in CH₂Cl₂ (1 L). Tetrazole diisopropylamine (7.1 g) and 2-cyanoethoxy-tetra-(isopropyl) phosphite (40.5 mL, 0.123 M) were added with stirring, under a nitrogen atmosphere. The resulting mixture was stirred for 20 hours at room temperature (TLC showed the reaction to be 95% complete). The reaction mixture was extracted with saturated NaHCO₃ (1×300 mL) and saturated NaCl (3×300 mL). The aqueous washes were back-extracted with CH₂Cl₂ (300 mL), and the extracts were combined, dried over MgSO₄ and concentrated. The residue obtained was chromatographed on a 1.5 kg silica column using EtOAc/hexane (3:1) as the eluting solvent. The pure fractions were combined to give 90.6 g (87%) of the title compound.

[0165] 2′-O-(Aminooxyethyl) Nucleoside Amidites and 2′-O-(dimethylaminooxyethyl) Nucleoside Amidites

[0166] 2′-(Dimethylaminooxyethoxy) Nucleoside Amidites

[0167] 2′-(Dimethylaminooxyethoxy) nucleoside amidites [also known in the art as 2′-O-(dimethylaminooxyethyl) nucleoside amidites] are prepared as described in the following paragraphs. Adenosine, cytidine and guanosine nucleoside amidites are prepared similarly to the thymidine (5-methyluridine) except the exocyclic amines are protected with a benzoyl moiety in the case of adenosine and cytidine and with isobutyryl in the case of guanosine.

[0168] 5′-O-tert-Butyldiphenylsilyl-O²-2′-anhydro-5-methyluridine

[0169] O²-2′-anhydro-5-methyluridine (Pro. Bio. Sint., Varese, Italy, 100.0 g, 0.416 mmol), dimethylaminopyridine (0.66 g, 0.013 eq, 0.0054 mmol) were dissolved in dry pyridine (500 ml) at ambient temperature under an argon atmosphere and with mechanical stirring. tert-Butyldiphenylchlorosilane (125.8 g, 119.0 mL, 1.1 eq, 0.458 mmol) was added in one portion. The reaction was stirred for 16 h at ambient temperature. TLC (Rf 0.22, ethyl acetate) indicated a complete reaction. The solution was concentrated under reduced pressure to a thick oil. This was partitioned between dichloromethane (1 L) and saturated sodium bicarbonate (2×1 L) and brine (1 L). The organic layer was dried over sodium sulfate and concentrated under reduced pressure to a thick oil. The oil was dissolved in a 1:1 mixture of ethyl acetate and ethyl ether (600 mL) and the solution was cooled to −10° C. The resulting crystalline product was collected by filtration, washed with ethyl ether (3×200 mL) and dried (40° C., 1 mm Hg, 24 h) to 149 g (74.8%) of white solid. TLC and NMR were consistent with pure product.

[0170] 5′-O-tert-Butyldiphenylsilyl-2′-O-(2-hydroxyethyl)-5-methyluridine

[0171] In a 2 L stainless steel, unstirred pressure reactor was added borane in tetrahydrofuran (1.0 M, 2.0 eq, 622 mL). In the fume hood and with manual stirring, ethylene glycol (350 mL, excess) was added cautiously at first until the evolution of hydrogen gas subsided. 5′-O-tert-Butyldiphenylsilyl-O²-2′-anhydro-5-methyluridine (149 g, 0.311 mol) and sodium bicarbonate (0.074 g, 0.003 eq) were added with manual stirring. The reactor was sealed and heated in an oil bath until an internal temperature of 160° C. was reached and then maintained for 16 h (pressure<100 psig). The reaction vessel was cooled to ambient and opened. TLC (Rf 0.67 for desired product and Rf 0.82 for ara-T side product, ethyl acetate) indicated about 70% conversion to the product. In order to avoid additional side product formation, the reaction was stopped, concentrated under reduced pressure (10 to 1 mm Hg) in a warm water bath (40-100° C.) with the more extreme conditions used to remove the ethylene glycol. [Alternatively, once the low boiling solvent is gone, the remaining solution can be partitioned between ethyl acetate and water. The product will be in the organic phase.] The residue was purified by column chromatography (2 kg silica gel, ethyl acetate-hexanes gradient 1:1 to 4:1). The appropriate fractions were combined, stripped and dried to product as a white crisp foam (84 g, 50%), contaminated starting material (17.4 g) and pure reusable starting material 20 g. The yield based on starting material less pure recovered starting material was 58%. TLC and NMR were consistent with 99% pure product.

[0172] 2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine

[0173] 5′-O-tert-Butyldiphenylsilyl-2′-O-(2-hydroxyethyl)-5-methyluridine (20 g, 36.98 mmol) was mixed with triphenylphosphine (11.63 g, 44.36 mmol) and N-hydroxyphthalimide (7.24 g, 44.36 mmol). It was then dried over P₂O₅ under high vacuum for two days at 40° C. The reaction mixture was flushed with argon and dry THF (369.8 mL, Aldrich, sure seal bottle) was added to get a clear solution. Diethyl-azodicarboxylate (6.98 mL, 44.36 mmol) was added dropwise to the reaction mixture. The rate of addition is maintained such that resulting deep red coloration is just discharged before adding the next drop. After the addition was complete, the reaction was stirred for 4 hrs. By that time TLC showed the completion of the reaction (ethylacetate:hexane, 60:40). The solvent was evaporated in vacuum. Residue obtained was placed on a flash column and eluted with ethyl acetate:hexane (60:40), to get 2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine as white foam (21.819 g, 86%).

[0174] 5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy)ethyl]-5-methyluridine

[0175] 2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine (3.1 g, 4.5 mmol) was dissolved in dry CH₂Cl₂ (4.5 mL) and methylhydrazine (300 mL, 4.64 mmol) was added dropwise at −10° C. to 0° C. After 1 h the mixture was filtered, the filtrate was washed with ice cold CH₂Cl₂ and the combined organic phase was washed with water, brine and dried over anhydrous Na₂SO₄. The solution was concentrated to get 2′-O-(aminooxyethyl) thymidine, which was then dissolved in MeOH (67.5 mL). To this formaldehyde (20% aqueous solution, w/w, 1.1 eq.) was added and the resulting mixture was strirred for 1 h. Solvent was removed under vacuum; residue chromatographed to get 5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy) ethyl]-5-methyluridine as white foam (1.95 g, 78%).

[0176] 5′-O-tert-Butyldiphenylsilyl-2′-O-[N,N-dimethylaminooxyethyl]-5-methyluridine

[0177] 5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy)ethyl]-5-methyluridine (1.77 g, 3.12 mmol) was dissolved in a solution of 1M pyridinium p-toluenesulfonate (PPTS) in dry MeOH (30.6 mL). Sodium cyanoborohydride (0.39 g, 6.13 mmol) was added to this solution at 10° C. under inert atmosphere. The reaction mixture was stirred for 10 minutes at 10° C. After that the reaction vessel was removed from the ice bath and stirred at room temperature for 2 h, the reaction monitored by TLC (5% MeOH in CH₂Cl₂). Aqueous NaHCO₃ solution (5%, 10 mL) was added and extracted with ethyl acetate (2×20 mL). Ethyl acetate phase was dried over anhydrous Na₂SO₄, evaporated to dryness. Residue was dissolved in a solution of 1M PPTS in MeOH (30.6 mL). Formaldehyde (20% w/w, 30 mL, 3.37 mmol) was added and the reaction mixture was stirred at room temperature for 10 minutes. Reaction mixture cooled to 10° C. in an ice bath, sodium cyanoborohydride (0.39 g, 6.13 mmol) was added and reaction mixture stirred at 10° C. for 10 minutes. After 10 minutes, the reaction mixture was removed from the ice bath and stirred at room temperature for 2 hrs. To the reaction mixture 5% NaHCO₃ (25 mL) solution was added and extracted with ethyl acetate (2×25 mL). Ethyl acetate layer was dried over anhydrous Na₂SO₄ and evaporated to dryness. The residue obtained was purified by flash column chromatography and eluted with 5% MeOH in CH₂Cl₂ to get 5′-O-tert-butyldiphenylsilyl-2′-O-[N,N-dimethylaminooxyethyl]-5-methyluridine as a white foam (14.6 g, 80%).

[0178] 2′-O-(dimethylaminooxyethyl)-5-methyluridine

[0179] Triethylamine trihydrofluoride (3.91 mL, 24.0 mmol) was dissolved in dry THF and triethylamine (1.67 mL, 12 mmol, dry, kept over KOH). This mixture of triethylamine-2HF was then added to 5′-O-tert-butyldiphenylsilyl-2′-O-[N,N-dimethylaminooxyethyl]-5-methyluridine (1.40 g, 2.4 mmol) and stirred at room temperature for 24 hrs. Reaction was monitored by TLC (5% MeOH in CH₂Cl₂). Solvent was removed under vacuum and the residue placed on a flash column and eluted with 10% MeOH in CH₂Cl₂ to get 2′-O-(dimethylaminooxyethyl)-5-methyluridine (766 mg, 92.5%).

[0180] 5′-O-DMT-2′-O-(dimethylaminooxyethyl)-5-methyluridine

[0181] 2′-O-(dimethylaminooxyethyl)-5-methyluridine (750 mg, 2.17 mmol) was dried over P₂O₅ under high vacuum overnight at 40° C. It was then co-evaporated with anhydrous pyridine (20 mL). The residue obtained was dissolved in pyridine (11 mL) under argon atmosphere. 4-dimethylaminopyridine (26.5 mg, 2.60 mmol), 4,4′-dimethoxytrityl chloride (880 mg, 2.60 mmol) was added to the mixture and the reaction mixture was stirred at room temperature until all of the starting material disappeared. Pyridine was removed under vacuum and the residue chromatographed and eluted with 10% MeOH in CH₂Cl₂ (containing a few drops of pyridine) to get 5′-O-DMT-2′-O-(dimethylamino-oxyethyl)-5-methyluridine (1.13 g, 80%).

[0182] 5′-O-DMT-2′-O-(2-N,N-dimethylaminooxyethyl)-5-methyluridine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite]

[0183] 5′-O-DMT-2′-O-(dimethylaminooxyethyl)-5-methyluridine (1.08 g, 1.67 mmol) was co-evaporated with toluene (20 mL). To the residue N,N-diisopropylamine tetrazonide (0.29 g, 1.67 mmol) was added and dried over P₂O₅ under high vacuum overnight at 40° C. Then the reaction mixture was dissolved in anhydrous acetonitrile (8.4 mL) and 2-cyanoethyl-N,N,N¹, N¹-tetraisopropylphosphoramidite (2.12 mL, 6.08 mmol) was added. The reaction mixture was stirred at ambient temperature for 4 hrs under inert atmosphere. The progress of the reaction was monitored by TLC (hexane:ethyl acetate 1:1). The solvent was evaporated, then the residue was dissolved in ethyl acetate (70 mL) and washed with 5% aqueous NaHCO₃ (40 mL). Ethyl acetate layer was dried over anhydrous Na₂SO₄ and concentrated. Residue obtained was chromatographed (ethyl acetate as eluent) to get 5′-O-DMT-2′-O-(2-N,N-dimethylaminooxyethyl)-5-methyluridine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite] as a foam (1.04 g, 74.9%).

[0184] 2′-(Aminooxyethoxy) Nucleoside Amidites

[0185] 2′-(Aminooxyethoxy) nucleoside amidites [also known in the art as 2′-O-(aminooxyethyl) nucleoside amidites] are prepared as described in the following paragraphs. Adenosine, cytidine and thymidine nucleoside amidites are prepared similarly.

[0186] N2-isobutyryl-6-O-diphenylcarbamoyl-2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl) guanosine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite]

[0187] The 2′-O-aminooxyethyl guanosine analog may be obtained by selective 2′-O-alkylation of diaminopurine riboside. Multigram quantities of diaminopurine riboside may be purchased from Schering AG (Berlin) to provide 2′-O-(2-ethylacetyl) diaminopurine riboside along with a minor amount of the 3′-O-isomer. 2′-O-(2-ethylacetyl) diaminopurine riboside may be resolved and converted to 2′-O-(2-ethylacetyl) guanosine by treatment with adenosine deaminase. (McGee, D. P. C., Cook, P. D., Guinosso, C. J., WO 94/02501 A1 940203.) Standard protection procedures should afford 2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl) guanosine and 2-N-isobutyryl-6-O-diphenylcarbamoyl-2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl) guanosine which may be reduced to provide 2-N-isobutyryl-6-O-diphenylcarbamoyl-2′-O-(2-hydroxyethyl)-5′-O-(4,4′-dimethoxytrityl) guanosine. As before the hydroxyl group may be displaced by N-hydroxyphthalimide via a Mitsunobu reaction, and the protected nucleoside may phosphitylated as usual to yield 2-N-isobutyryl-6-O-diphenylcarbamoyl-2′-O-([2-phthalmidoxy]ethyl)-5′-O-(4,4′-dimethoxytrityl) guanosine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite].

[0188] 2′-dimethylaminoethoxyethoxy (2′-DMAEOE) Nucleoside Amidites

[0189] 2′-dimethylaminoethoxyethoxy nucleoside amidites (also known in the art as 2′-O-dimethylaminoethoxyethyl, i.e., 2′-O—CH₂—O—CH₂—N(CH₂)₂, or 2′-DMAEOE nucleoside amidites) are prepared as follows. Other nucleoside amidites are prepared similarly.

[0190] 2′-O-[2(2-N,N-dimethylaminoethoxy)ethyl]-5-methyl Uridine

[0191] 2[2-(Dimethylamino)ethoxy]ethanol (Aldrich, 6.66 g, 50 mmol) is slowly added to a solution of borane in tetra-hydrofuran (1 M, 10 mL, 10 mmol) with stirring in a 100 mL bomb. Hydrogen gas evolves as the solid dissolves. O²-,2′-anhydro-5-methyluridine (1.2 g, 5 mmol), and sodium bicarbonate (2.5 mg) are added and the bomb is sealed, placed in an oil bath and heated to 155° C. for 26 hours. The bomb is cooled to room temperature and opened. The crude solution is concentrated and the residue partitioned between water (200 mL) and hexanes (200 mL). The excess phenol is extracted into the hexane layer. The aqueous layer is extracted with ethyl acetate (3×200 mL) and the combined organic layers are washed once with water, dried over anhydrous sodium sulfate and concentrated. The residue is columned on silica gel using methanol/methylene chloride 1:20 (which has 2% triethylamine) as the eluent. As the column fractions are concentrated a colorless solid forms which is collected to give the title compound as a white solid.

[0192] 5′-O-dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy) ethyl)]-5-methyl Uridine

[0193] To 0.5 g (1.3 mmol) of 2′-O-[2(2-N,N-dimethylamino-ethoxy)ethyl)]-5-methyl uridine in anhydrous pyridine (8 mL), triethylamine (0.36 mL) and dimethoxytrityl chloride (DMT-Cl, 0.87 g, 2 eq.) are added and stirred for 1 hour. The reaction mixture is poured into water (200 mL) and extracted with CH₂Cl₂ (2×200 mL). The combined CH₂Cl₂ layers are washed with saturated NaHCO₃ solution, followed by saturated NaCl solution and dried over anhydrous sodium sulfate. Evaporation of the solvent followed by silica gel chromatography using MeOH:CH₂Cl₂:Et₃N (20:1, v/v, with 1% triethylamine) gives the title compound.

[0194] 5′-O-Dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy)-ethyl)]-5-methyl uridine-3′-O-(cyanoethyl-N,N-diisopropyl) phosphoramidite

[0195] Diisopropylaminotetrazolide (0.6 g) and 2-cyanoethoxy-N,N-diisopropyl phosphoramidite (1.1 mL, 2 eq.) are added to a solution of 5′-O-dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy)ethyl)]-5-methyluridine (2.17 g, 3 mmol) dissolved in CH₂Cl₂ (20 mL) under an atmosphere of argon. The reaction mixture is stirred overnight and the solvent evaporated. The resulting residue is purified by silica gel flash column chromatography with ethyl acetate as the eluent to give the title compound.

Example 2

[0196] Oligonucleotide Synthesis

[0197] Unsubstituted and substituted phosphodiester (P═O) oligonucleotides are synthesized on an automated DNA synthesizer (Applied Biosystems model 380B) using standard phosphoramidite chemistry with oxidation by iodine.

[0198] Phosphorothioates (P═S) are synthesized as for the phosphodiester oligonucleotides except the standard oxidation bottle was replaced by 0.2 M solution of 3H-1,2-benzodithiole-3-one 1,1-dioxide in acetonitrile for the stepwise thiation of the phosphite linkages. The thiation wait step was increased to 68 sec and was followed by the capping step. After cleavage from the CPG column and deblocking in concentrated ammonium hydroxide at 55° C. (18 h), the oligonucleotides were purified by precipitating twice with 2.5 volumes of ethanol from a 0.5 M NaCl solution.

[0199] Phosphinate oligonucleotides are prepared as described in U.S. Pat. No. 5,508,270, herein incorporated by reference.

[0200] Alkyl phosphonate oligonucleotides are prepared as described in U.S. Pat. No. 4,469,863, herein incorporated by reference.

[0201] 3′-Deoxy-3′-methylene phosphonate oligonucleotides are prepared as described in U.S. Pat. Nos. 5,610,289 or 5,625,050, herein incorporated by reference.

[0202] Phosphoramidite oligonucleotides are prepared as described in U.S. Patent, 5,256,775 or U.S. Pat. No. 5,366,878, herein incorporated by reference.

[0203] Alkylphosphonothioate oligonucleotides are prepared as described in published PCT applications PCT/US94/00902 and PCT/US93/06976 (published as WO 94/17093 and WO 94/02499, respectively), herein incorporated by reference. 3′-Deoxy-3′-amino phosphoramidate oligonucleotides are prepared as described in U.S. Pat. No. 5,476,925, herein incorporated by reference.

[0204] Phosphotriester oligonucleotides are prepared as described in U.S. Pat. No. 5,023,243, herein incorporated by reference.

[0205] Borano phosphate oligonucleotides are prepared as described in U.S. Pat. Nos. 5,130,302 and 5,177,198, both herein incorporated by reference.

Example 3

[0206] Oligonucleoside Synthesis

[0207] Methylenemethylimino linked oligonucleosides, also identified as MMI linked oligonucleosides, methylenedimethyl-hydrazo linked oligonucleosides, also identified as MDH linked oligonucleosides, and methylenecarbonylamino linked oligonucleosides, also identified as amide-3 linked oligonucleosides, and methyleneaminocarbonyl linked oligonucleosides, also identified as amide-4 linked oligonucleosides, as well as mixed backbone compounds having, for instance, alternating MMI and P═O or P═S linkages are prepared as described in U.S. Pat. Nos. 5,378,825, 5,386,023, 5,489,677, 5,602,240 and 5,610,289, all of which are herein incorporated by reference.

[0208] Formacetal and thioformacetal linked oligonucleosides are prepared as described in U.S. Pat. Nos. 5,264,562 and 5,264,564, herein incorporated by reference.

[0209] Ethylene oxide linked oligonucleosides are prepared as described in U.S. Pat. No. 5,223,618, herein incorporated by reference.

Example 4

[0210] PNA Synthesis

[0211] Peptide nucleic acids (PNAs) are prepared in accordance with any of the various procedures referred to in Peptide Nucleic Acids (PNA): Synthesis, Properties and Potential Applications, Bioorganic & Medicinal Chemistry, 1996, 4, 5-23. They may also be prepared in accordance with U.S. Pat. Nos. 5,539,082, 5,700,922, and 5,719,262, herein incorporated by reference.

Example 5

[0212] Synthesis of Chimeric Oligonucleotides

[0213] Chimeric oligonucleotides, oligonucleosides or mixed oligonucleotides/oligonucleosides of the invention can be of several different types. These include a first type wherein the “gap” segment of linked nucleosides is positioned between 5′ and 3′ “wing” segments of linked nucleosides and a second “open end” type wherein the “gap” segment is located at either the 3′ or the 5′ terminus of the oligomeric compound. Oligonucleotides of the first type are also known in the art as “gapmers” or gapped oligonucleotides. Oligonucleotides of the second type are also known in the art as “hemimers” or “wingmers”.

[0214] [2′-O-Me]-[2′-deoxy]-[2′-O-Me] Chimeric Phosphorothioate Oligonucleotides

[0215] Chimeric oligonucleotides having 2′-O-alkyl phosphorothioate and 2′-deoxy phosphorothioate oligonucleotide segments are synthesized using an Applied Biosystems automated DNA synthesizer Model 380B, as above. Oligonucleotides are synthesized using the automated synthesizer and 2′-deoxy-5′-dimethoxytrityl-3′-O-phosphor-amidite for the DNA portion and 5′-dimethoxytrityl-2′-O-methyl-3′-O-phosphoramidite for 5′ and 3′ wings. The standard synthesis cycle is modified by increasing the wait step after the delivery of tetrazole and base to 600 s repeated four times for RNA and twice for 2′-O-methyl. The fully protected oligonucleotide is cleaved from the support and the phosphate group is deprotected in 3:1 ammonia/ethanol at room temperature overnight then lyophilized to dryness. Treatment in methanolic ammonia for 24 hrs at room temperature is then done to deprotect all bases and sample was again lyophilized to dryness. The pellet is resuspended in 1M TBAF in THF for 24 hrs at room temperature to deprotect the 2′ positions. The reaction is then quenched with 1M TEAA and the sample is then reduced to ½ volume by rotovac before being desalted on a G25 size exclusion column. The oligo recovered is then analyzed spectrophotometrically for yield and for purity by capillary electrophoresis and by mass spectrometry.

[0216] [2′-O-(2-Methoxyethyl)]-[2′-deoxy]-[2′-O-(Methoxyethyl)] Chimeric Phosphorothioate Oligonucleotides

[0217] [2′-O-(2-methoxyethyl)]—[2′-deoxy]—[-21-O-(methoxy-ethyl)] chimeric phosphorothioate oligonucleotides were prepared as per the procedure above for the 2′-O-methyl chimeric oligonucleotide, with the substitution of 2′-0-(methoxyethyl) amidites for the 2′-O-methyl amidites.

[0218] [2′-O-(2-Methoxyethyl) Phosphodiester]-[2′-deoxy Phosphorothioate]-[2′-O-(2-Methoxyethyl) Phosphodiester] Chimeric Oligonucleotides

[0219] [2′-O-(2-methoxyethyl phosphodiester]-[2′-deoxy phosphorothioate]-[2′-O-(methoxyethyl) phosphodiester] chimeric oligonucleotides are prepared as per the above procedure for the 2′-O-methyl chimeric oligonucleotide with the substitution of 2′-O-(methoxyethyl) amidites for the 2′-O-methylamidites, oxidization with iodine to generate the phosphodiester internucleotide linkages within the wing portions of the chimeric structures and sulfurization utilizing 3, H-1,2 benzodithiole-3-one 1,1 dioxide (Beaucage Reagent) to generate the phosphorothioate internucleotide linkages for the center gap.

[0220] Other chimeric oligonucleotides, chimeric oligonucleosides and mixed chimeric oligonucleotides/oligonucleosides are synthesized according to U.S. Pat. No. 5,623,065, herein incorporated by reference.

Example 6

[0221] Oligonucleotide Isolation

[0222] After cleavage from the controlled pore glass column (Applied Biosystems) and deblocking in concentrated ammonium hydroxide at 55° C. for 18 hours, the oligonucleotides or oligonucleosides are purified by precipitation twice out of 0.5 M NaCl with 2.5 volumes ethanol. Synthesized oligonucleotides were analyzed by polyacrylamide gel electrophoresis on denaturing gels and judged to be at least 85% full length material. The relative amounts of phosphorothioate and phosphodiester linkages obtained in synthesis were periodically checked by 31P nuclear magnetic resonance spectroscopy, and for some studies oligonucleotides were purified by HPLC, as described by Chiang et al., J. Biol. Chem. 1991, 266, 18162-18171. Results obtained with HPLC-purified material were similar to those obtained with non-HPLC purified material.

Example 7

[0223] Oligonucleotide Synthesis—96 Well Plate Format

[0224] Oligonucleotides were synthesized via solid phase P (III) phosphoramidite chemistry on an automated synthesizer capable of assembling 96 sequences simultaneously in a standard 96 well format. Phosphodiester internucleotide linkages were afforded by oxidation with aqueous iodine. Phosphorothioate internucleotide linkages were generated by sulfurization utilizing 3, H-1,2 benzodithiole-3-one 1,1 dioxide (Beaucage Reagent) in anhydrous acetonitrile. Standard base-protected beta-cyanoethyldiisopropyl phosphoramidites were purchased from commercial vendors (e.g. PE-Applied Biosystems, Foster City, Calif., or Pharmacia, Piscataway, N.J.). Non-standard nucleosides are synthesized as per known literature or patented methods. They are utilized as base protected beta-cyanoethyldiisopropyl phosphoramidites.

[0225] Oligonucleotides were cleaved from support and deprotected with concentrated NH₄OH at elevated temperature (55-60° C.) for 12-16 hours and the released product then dried in vacuo. The dried product was then re-suspended in sterile water to afford a master plate from which all analytical and test plate samples are then diluted utilizing robotic pipettors.

Example 8

[0226] Oligonucleotide Analysis—96 Well Plate Format

[0227] The concentration of oligonucleotide in each well was assessed by dilution of samples and UV absorption spectroscopy. The full-length integrity of the individual products was evaluated by capillary electrophoresis (CE) in either the 96 well format (Beckman P/ACE™ MDQ) or, for individually prepared samples, on a commercial CE apparatus (e.g., Beckman P/ACE™ 5000, ABI 270). Base and backbone composition was confirmed by mass analysis of the compounds utilizing electrospray-mass spectroscopy. All assay test plates were diluted from the master plate using single and multi-channel robotic pipettors. Plates were judged to be acceptable if at least 85% of the compounds on the plate were at least 85% full length.

Example 9

[0228] Cell Culture and Oligonucleotide Treatment

[0229] The effect of antisense compounds on target nucleic acid expression can be tested in any of a variety of cell types provided that the target nucleic acid is present at measurable levels. This can be routinely determined using, for example, PCR or Northern blot analysis. The following 4 cell types are provided for illustrative purposes, but other cell types can be routinely used, provided that the target is expressed in the cell type chosen. This can be readily determined by methods routine in the art, for example Northern blot analysis, Ribonuclease protection assays, or RT-PCR.

[0230] T-24 Cells:

[0231] The human transitional cell bladder carcinoma cell line T-24 was obtained from the American Type Culture Collection (ATCC) (Manassas, Va.). T-24 cells were routinely cultured in complete McCoy's 5A basal media (Invitrogen Corporation, Carlsbad, Calif.) supplemented with 10% fetal calf serum ((Invitrogen Corporation, Carlsbad, Calif.), penicillin 100 units per mL, and streptomycin 100 micrograms per mL (Invitrogen Corporation, Carlsbad, Calif.). Cells were routinely passaged by trypsinization and dilution when they reached 90% confluence. Cells were seeded into 96-well plates (Falcon-Primaria #3872) at a density of 7000 cells/well for use in RT-PCR analysis.

[0232] For Northern blotting or other analysis, cells may be seeded onto 100 mm or other standard tissue culture plates and treated similarly, using appropriate volumes of medium and oligonucleotide.

[0233] A549 Cells:

[0234] The human lung carcinoma cell line A549 was obtained from the American Type Culture Collection (ATCC) (Manassas, Va.). A549 cells were routinely cultured in DMEM basal media (Invitrogen Corporation, Carlsbad, Calif.) supplemented with 10% fetal calf serum (Invitrogen Corporation, Carlsbad, Calif.), penicillin 100 units per mL, and streptomycin 100 micrograms per mL (Invitrogen Corporation, Carlsbad, Calif.). Cells were routinely passaged by trypsinization and dilution when they reached 90% confluence.

[0235] NHDF Cells:

[0236] Human neonatal dermal fibroblast (NHDF) were obtained from the Clonetics Corporation (Walkersville, Md.). NHDFs were routinely maintained in Fibroblast Growth Medium (Clonetics Corporation, Walkersville, Md.) supplemented as recommended by the supplier. Cells were maintained for up to 10 passages as recommended by the supplier.

[0237] HEK Cells:

[0238] Human embryonic keratinocytes (HEK) were obtained from the Clonetics Corporation (Walkersville, Md.). HEKs were routinely maintained in Keratinocyte Growth Medium (Clonetics Corporation, Walkersville, Md.) formulated as recommended by the supplier. Cells were routinely maintained for up to 10 passages as recommended by the supplier.

[0239] Treatment With Antisense Compounds:

[0240] When cells reached 70% confluency, they were treated with oligonucleotide. For cells grown in 96-well plates, wells were washed once with 100 μL OPTI-MEM™-1 reduced-serum medium (Invitrogen Corporation, Carlsbad, Calif.) and then treated with 130 μL of OPTI-MEM™-1 containing 3.75 μg/mL LIPOFECTIN™ (Invitrogen Corporation, Carlsbad, Calif.) and the desired concentration of oligonucleotide. After 4-7 hours of treatment, the medium was replaced with fresh medium. Cells were harvested 16-24 hours after oligonucleotide treatment.

[0241] The concentration of oligonucleotide used varies from cell line to cell line. To determine the optimal oligonucleotide concentration for a particular cell line, the cells are treated with a positive control oligonucleotide at a range of concentrations. For human cells the positive control oligonucleotide is ISIS 13920, TCCGTCATCGCTCCTCAGGG, SEQ ID NO: 1, a 2′-O-methoxyethyl gapmer (2′-O-methoxyethyls shown in bold) with a phosphorothioate backbone which is targeted to human H-ras. For mouse or rat cells the positive control oligonucleotide is ISIS 15770, ATGCATTCTGCCCCCAAGGA, SEQ ID NO: 2, a 2′-O-methoxyethyl gapmer (2′-O-methoxyethyls shown in bold) with a phosphorothioate backbone which is targeted to both mouse and rat c-raf. The concentration of positive control oligonucleotide that results in 80% inhibition of c-Ha-ras (for ISIS 13920) or c-raf (for ISIS 15770) mRNA is then utilized as the screening concentration for new oligonucleotides in subsequent experiments for that cell line. If 80% inhibition is not achieved, the lowest concentration of positive control oligonucleotide that results in 60% inhibition of H-ras or c-raf mRNA is then utilized as the oligonucleotide screening concentration in subsequent experiments for that cell line. If 60% inhibition is not achieved, that particular cell line is deemed as unsuitable for oligonucleotide transfection experiments.

Example 10

[0242] Analysis of Oligonucleotide Inhibition of Hematopoietic Cell Protein Tyrosine Kinase Expression

[0243] Antisense modulation of hematopoietic cell protein tyrosine kinase expression can be assayed in a variety of ways known in the art. For example, hematopoietic cell protein tyrosine kinase mRNA levels can be quantitated by, e.g., Northern blot analysis, competitive polymerase chain reaction (PCR), or real-time PCR (RT-PCR). Real-time quantitative PCR is presently preferred. RNA analysis can be performed on total cellular RNA or poly(A)+mRNA. The preferred method of RNA analysis of the present invention is the use of total cellular RNA as described in other examples herein. Methods of RNA isolation are taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 1, pp. 4.1.1-4.2.9 and 4.5.1-4.5.3, John Wiley & Sons, Inc., 1993. Northern blot analysis is routine in the art and is taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 1, pp. 4.2.1-4.2.9, John Wiley & Sons, Inc., 1996. Real-time quantitative (PCR) can be conveniently accomplished using the commercially available ABI PRISM™ 7700 Sequence Detection System, available from PE-Applied Biosystems, Foster City, Calif. and used according to manufacturer's instructions.

[0244] Protein levels of hematopoietic cell protein tyrosine kinase can be quantitated in a variety of ways well known in the art, such as immunoprecipitation, Western blot analysis (immunoblotting), ELISA or fluorescence-activated cell sorting (FACS). Antibodies directed to hematopoietic cell protein tyrosine kinase can be identified and obtained from a variety of sources, such as the MSRS catalog of antibodies (Aerie Corporation, Birmingham, Mich.), or can be prepared via conventional antibody generation methods. Methods for preparation of polyclonal antisera are taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 11.12.1-11.12.9, John Wiley & Sons, Inc., 1997. Preparation of monoclonal antibodies is taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 11.4.1-11.11.5, John Wiley & Sons, Inc., 1997.

[0245] Immunoprecipitation methods are standard in the art and can be found at, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 10.16.1-10.16.11, John Wiley & Sons, Inc., 1998. Western blot (immunoblot) analysis is standard in the art and can be found at, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 10.8.1-10.8.21, John Wiley & Sons, Inc., 1997. Enzyme-linked immunosorbent assays (ELISA) are standard in the art and can be found at, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 11.2.1-11.2.22, John Wiley & Sons, Inc., 1991.

Example 11

[0246] Poly(A)+mRNA Isolation

[0247] Poly(A)+mRNA was isolated according to Miura et al., Clin. Chem., 1996, 42, 1758-1764. Other methods for poly(A)+mRNA isolation are taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 1, pp. 4.5.1-4.5.3, John Wiley & Sons, Inc., 1993. Briefly, for cells grown on 96-well plates, growth medium was removed from the cells and each well was washed with 200 μL cold PBS. 60 μL lysis buffer (10 mM Tris-HCl, pH 7.6, 1 mM EDTA, 0.5 M NaCl, 0.5% NP-40, 20 mM vanadyl-ribonucleoside complex) was added to each well, the plate was gently agitated and then incubated at room temperature for five minutes. 55 μL of lysate was transferred to Oligo d (T) coated 96-well plates (AGCT Inc., Irvine Calif.). Plates were incubated for 60 minutes at room temperature, washed 3 times with 200 μL of wash buffer (10 mM Tris-HCl pH 7.6, 1 mM EDTA, 0.3 M NaCl). After the final wash, the plate was blotted on paper towels to remove excess wash buffer and then air-dried for 5 minutes. 60 μL of elution buffer (5 mM Tris-HCl pH 7.6), preheated to 70° C. was added to each well, the plate was incubated on a 90° C. hot plate for 5 minutes, and the eluate was then transferred to a fresh 96-well plate.

[0248] Cells grown on 100 mm or other standard plates may be treated similarly, using appropriate volumes of all solutions.

Example 12

[0249] Total RNA Isolation

[0250] Total RNA was isolated using an RNEASY 96™ kit and buffers purchased from Qiagen Inc. (Valencia, Calif.) following the manufacturer's recommended procedures. Briefly, for cells grown on 96-well plates, growth medium was removed from the cells and each well was washed with 200 μL cold PBS. 150 μL Buffer RLT was added to each well and the plate vigorously agitated for 20 seconds. 150 μL of 70% ethanol was then added to each well and the contents mixed by pipetting three times up and down. The samples were then transferred to the RNEASY 96™ well plate attached to a QIAVAC™ manifold fitted with a waste collection tray and attached to a vacuum source. Vacuum was applied for 1 minute. 500 μL of Buffer RW1 was added to each well of the RNEASY 96™ plate and incubated for 15 minutes and the vacuum was again applied for 1 minute. An additional 500 μL of Buffer RW1 was added to each well of the RNEASY 96™ plate and the vacuum was applied for 2 minutes. 1 mL of Buffer RPE was then added to each well of the RNEASY 96™ plate and the vacuum applied for a period of 90 seconds. The Buffer RPE wash was then repeated and the vacuum was applied for an additional 3 minutes. The plate was then removed from the QIAVAC™ manifold and blotted dry on paper towels. The plate was then re-attached to the QIAVAC™ manifold fitted with a collection tube rack containing 1.2 mL collection tubes. RNA was then eluted by pipetting 170 μL water into each well, incubating 1 minute, and then applying the vacuum for 3 minutes.

[0251] The repetitive pipetting and elution steps may be automated using a QIAGEN Bio-Robot 9604 (Qiagen, Inc., Valencia Calif.). Essentially, after lysing of the cells on the culture plate, the plate is transferred to the robot deck where the pipetting, DNase treatment and elution steps are carried out.

Example 13

[0252] Real-time Quantitative PCR Analysis of Hematopoietic Cell Protein Tyrosine Kinase mRNA Levels

[0253] Quantitation of hematopoietic cell protein tyrosine kinase mRNA levels was determined by real-time quantitative PCR using the ABI PRISM™ 7700 Sequence Detection System (PE-Applied Biosystems, Foster City, Calif.) according to manufacturer's instructions. This is a closed-tube, non-gel-based, fluorescence detection system which allows high-throughput quantitation of polymerase chain reaction (PCR) products in real-time. As opposed to standard PCR, in which amplification products are quantitated after the PCR is completed, products in real-time quantitative PCR are quantitated as they accumulate. This is accomplished by including in the PCR reaction an oligonucleotide probe that anneals specifically between the forward and reverse PCR primers, and contains two fluorescent dyes. A reporter dye (e.g., FAM, obtained from either Operon Technologies Inc., Alameda, Calif. or Integrated DNA Technologies Inc., Coralville, Iowa) is attached to the 5′ end of the probe and a quencher dye (e.g., TAMRA, obtained from either Operon Technologies Inc., Alameda, Calif. or Integrated DNA Technologies Inc., Coralville, Iowa) is attached to the 3′ end of the probe. When the probe and dyes are intact, reporter dye emission is quenched by the proximity of the 3′ quencher dye. During amplification, annealing of the probe to the target sequence creates a substrate that can be cleaved by the 5′-exonuclease activity of Taq polymerase. During the extension phase of the PCR amplification cycle, cleavage of the probe by Taq polymerase releases the reporter dye from the remainder of the probe (and hence from the quencher moiety) and a sequence-specific fluorescent signal is generated. With each cycle, additional reporter dye molecules are cleaved from their respective probes, and the fluorescence intensity is monitored at regular intervals by laser optics built into the ABI PRISM™ 7700 Sequence Detection System. In each assay, a series of parallel reactions containing serial dilutions of mRNA from untreated control samples generates a standard curve that is used to quantitate the percent inhibition after antisense oligonucleotide treatment of test samples.

[0254] Prior to quantitative PCR analysis, primer-probe sets specific to the target gene being measured are evaluated for their ability to be “multiplexed” with a GAPDH amplification reaction. In multiplexing, both the target gene and the internal standard gene GAPDH are amplified concurrently in a single sample. In this analysis, mRNA isolated from untreated cells is serially diluted. Each dilution is amplified in the presence of primer-probe sets specific for GAPDH only, target gene only (“single-plexing”), or both (multiplexing). Following PCR amplification, standard curves of GAPDH and target mRNA signal as a function of dilution are generated from both the single-plexed and multiplexed samples. If both the slope and correlation coefficient of the GAPDH and target signals generated from the multiplexed samples fall within 10% of their corresponding values generated from the single-plexed samples, the primer-probe set specific for that target is deemed multiplexable. Other methods of PCR are also known in the art.

[0255] PCR reagents were obtained from Invitrogen, Carlsbad, Calif. RT-PCR reactions were carried out by adding 20 μL PCR cocktail (2.5× PCR buffer (—MgCl2), 6.6 mM MgCl2, 375 μM each of dATP, dCTP, dCTP and dGTP, 375 nM each of forward primer and reverse primer, 125 nM of probe, 4 Units RNAse inhibitor, 1.25 Units PLATINUM® Taq, 5 Units MuLV reverse transcriptase, and 2.5× ROX dye) to 96 well plates containing 30 μL total RNA solution. The RT reaction was carried out by incubation for 30 minutes at 48° C. Following a 10 minute incubation at 95° C. to activate the PLATINUM® Taq, 40 cycles of a two-step PCR protocol were carried out: 95° C. for 15 seconds (denaturation) followed by 60° C. for 1.5 minutes (annealing/extension).

[0256] Gene target quantities obtained by real time RT-PCR are normalized using either the expression level of GAPDH, a gene whose expression is constant, or by quantifying total RNA using RiboGreen™ (Molecular Probes, Inc. Eugene, Oreg.). GAPDH expression is quantified by real time RT-PCR, by being run simultaneously with the target, multiplexing, or separately. Total RNA is quantified using RiboGreen™ RNA quantification reagent from Molecular Probes. Methods of RNA quantification by RiboGreen™ are taught in Jones, L. J., et al, Analytical Biochemistry, 1998, 265, 368-374.

[0257] In this assay, 170 μL of RiboGreen™ working reagent (RiboGreen™ reagent diluted 1:350 in 10 mM Tris-HCl, 1 mM EDTA, pH 7.5) is pipetted into a 96-well plate containing 30 μL purified, cellular RNA. The plate is read in a CytoFluor 4000 (PE Applied Biosystems) with excitation at 480 nm and emission at 520 nm.

[0258] Probes and primers to human hematopoietic cell protein tyrosine kinase were designed to hybridize to a human hematopoietic cell protein tyrosine kinase sequence, using published sequence information (GenBank accession number M16591.1, incorporated herein as SEQ ID NO:3). For human hematopoietic cell protein tyrosine kinase the PCR primers were:

[0259] forward primer: TTTGTCCGTGCGAGACTACG (SEQ ID NO: 4)

[0260] reverse primer: TTGTCCAGGGTCCGGATCT (SEQ ID NO: 5) and the

[0261] PCR probe was: FAM-CTCGGCAGGGAGATACCGTGAAACATTAC-TAMRA (SEQ ID NO: 6) where FAM (PE-Applied Biosystems, Foster City, Calif.) is the fluorescent reporter dye) and TAMPA (PE-Applied Biosystems, Foster City, Calif.) is the quencher dye. For human GAPDH the PCR primers were:

[0262] forward primer: GAAGGTGAAGGTCGGAGTC(SEQ ID NO:7)

[0263] reverse primer: GAAGATGGTGATGGGATTTC (SEQ ID NO:8) and the

[0264] PCR probe was: 5′ JOE-CAAGCTTCCCGTTCTCAGCC-TAMRA 3′ (SEQ ID NO: 9) where JOE (PE-Applied Biosystems, Foster City, Calif.) is the fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster City, Calif.) is the quencher dye.

Example 14

[0265] Northern Blot Analysis of Hematopoietic Cell Protein Tyrosine Kinase mRNA Levels

[0266] Eighteen hours after antisense treatment, cell monolayers were washed twice with cold PBS and lysed in 1 mL RNAZOL™ (TEL-TEST “B” Inc., Friendswood, Tex.). Total RNA was prepared following manufacturer's recommended protocols. Twenty micrograms of total RNA was fractionated by electrophoresis through 1.2% agarose gels containing 1.1% formaldehyde using a MOPS buffer system (AMRESCO, Inc. Solon, Ohio). RNA was transferred from the gel to HYBOND™-N+ nylon membranes (Amersham Pharmacia Biotech, Piscataway, N.J.) by overnight capillary transfer using a Northern/Southern Transfer buffer system (TEL-TEST “B” Inc., Friendswood, Tex.). RNA transfer was confirmed by UV visualization. Membranes were fixed by UV cross-linking using a STRATALINKER™ UV Crosslinker 2400 (Stratagene, Inc, La Jolla, Calif.) and then probed using QUICKHYB™ hybridization solution (Stratagene, La Jolla, Calif.) using manufacturer's recommendations for stringent conditions.

[0267] To detect human hematopoietic cell protein tyrosine kinase, a human hematopoietic cell protein tyrosine kinase specific probe was prepared by PCR using the forward primer TTTGTCCGTGCGAGACTACG (SEQ ID NO: 4) and the reverse primer TTGTCCAGGGTCCGGATCT (SEQ ID NO: 5). To normalize for variations in loading and transfer efficiency membranes were stripped and probed for human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) RNA (Clontech, Palo Alto, Calif.).

[0268] Hybridized membranes were visualized and quantitated using a PHOSPHORIMAGER™ and IMAGEQUANT™ Software V3.3 (Molecular Dynamics, Sunnyvale, Calif.). Data was normalized to GAPDH levels in untreated controls.

Example 15

[0269] Antisense Inhibition of Human Hematopoietic Cell Protein Tyrosine Kinase Expression by Chimeric Phosphorothioate Oligonucleotides Having 2′-MOE Wings and a Deoxy Gap

[0270] In accordance with the present invention, a series of oligonucleotides were designed to target different regions of the human hematopoietic cell protein tyrosine kinase RNA, using published sequences (GenBank accession number M16591.1, incorporated herein as SEQ ID NO: 3, and residues 1-30000 of GenBank accession number AL049539.2, representing a partial genomics sequence of hematopoietic cell protein tyrosine kinase, incorporated herein as SEQ ID NO: 10). The oligonucleotides are shown in Table 1. “Target site” indicates the first (5′-most) nucleotide number on the particular target sequence to which the oligonucleotide binds. All compounds in Table 1 are chimeric oligonucleotides (“gapmers”) 20 nucleotides in length, composed of a central “gap” region consisting of ten 2′-deoxynucleotides, which is flanked on both sides (5′ and 3′ directions) by five-nucleotide “wings”. The wings are composed of 2′-methoxyethyl (2¹-MOE) nucleotides. The internucleoside (backbone) linkages are phosphorothioate (P═S) throughout the oligonucleotide. All cytidine residues are 5-methylcytidines. The compounds were analyzed for their effect on human hematopoietic cell protein tyrosine kinase mRNA levels by quantitative real-time PCR as described in other examples herein. Data are averages from two experiments. If present, “N.D.” indicates “no data”. TABLE 1 Inhibition of human hematopoietic cell protein tyrosine kinase mRNA levels by chimeric phosphorothioate oligonucleotides having 2′-MOE wings and a deoxy gap TARGET SEQ ID TARGET SEQ ID ISIS # REGION NO SITE SEQUENCE % INHIB NO 150717 5′UTR 3 53 tcgtcatcgtcttcatctcc 0 11 150718 5′UTR 3 67 cctcagagccatcgtcgtca 6 12 150719 5′UTR 3 77 cctgaggtcccctcagagcc 31 13 150720 5′UTR 3 122 cagcccggatcctcgcagct 15 14 150721 5′UTR 3 125 gggcagcccggatcctcgca 9 15 150723 Coding 3 258 tggatgtgggatccggcacg 0 16 150724 Coding 3 283 tggctattaggccccggctt 22 17 150725 Coding 3 328 atgtcctcagagcctgcctc 72 18 150726 Coding 3 388 ttctggaagctgaggtcttc 31 19 150727 Coding 3 391 cccttctggaagctgaggtc 19 20 150728 Coding 3 466 tagccctccttccgggtggc 0 21 150729 Coding 3 535 ctgatgcccttgaaaaacca 28 22 150730 Coding 3 584 gcccagcatgttgccgggag 3 23 150731 Coding 3 589 aaggagcccagcatgttgcc 0 24 150732 Coding 3 592 atgaaggagcccagcatgtt 0 25 150733 Coding 3 596 gatcatgaaggagcccagca 0 26 150734 Coding 3 599 ccggatcatgaaggagccca 0 27 150735 Coding 3 636 cggacaaagagtagcttcct 0 28 150736 Coding 3 695 cagggtccggatcttgtaat 6 29 150737 Coding 3 778 tcgttccccttcttgtagtg 0 30 150738 Coding 3 799 gacagtttctggcagagccc 28 31 150739 Coding 3 814 gacatgcagggcaccgacag 27 32 150740 Coding 3 823 ggcttggaagacatgcaggg 19 33 150741 Coding 3 896 agctccaagtttcttctcca 21 34 150742 Coding 3 899 cccagctccaagtttcttct 19 35 150743 Coding 3 902 ctgcccagctccaagtttct 45 36 150744 Coding 3 926 ggtggccatccagacttccc 27 37 150745 Coding 3 934 ttgttgtaggtggccatcca 11 38 150746 Coding 3 939 tgtgcttgttgtaggtggcc 26 39 150747 Coding 3 942 tggtgtgcttgttgtaggtg 28 40 150748 Coding 3 979 gacatgctccctggcttcat 7 41 150749 Coding 3 993 ggaaggcctccaccgacatg 40 42 150750 Coding 3 1026 gctgcagagttttcatcacg 4 43 150751 Coding 3 1046 aagtttgaccagcttgtcat 6 44 150752 Coding 3 1088 ctccgtgatgatgtagatgg 5 45 150753 Coding 3 1131 catcacttttcagaaagtcc 7 46 150754 Coding 3 1145 ctgcttgctgccctcatcac 63 47 150755 Coding 3 1175 ggctgagaagtcaatgagtt 0 48 150756 Coding 3 1188 cttctgcaatctgggctgag 6 49 150757 Coding 3 1191 tgccttctgcaatctgggct 6 50 150758 Coding 3 1197 aggccatgccttctgcaatc 49 51 150759 Coding 3 1207 tgctcgatgaaggccatgcc 16 52 150760 Coding 3 1216 tagttcctctgctcgatgaa 36 53 150761 Coding 3 1226 tcggtggatgtagttcctct 0 54 150762 Coding 3 1282 tcagcaatcttacacaccag 0 55 150763 Coding 3 1301 gacccgggccaggccaaagt 0 56 150764 Coding 3 1315 tcgttgtcctcaatgacccg 25 57 150765 Coding 3 1342 aacttggccccttcccgagc 26 58 150766 Coding 3 1369 gcttcaggagctgtccactt 0 59 150767 Coding 3 1402 tctgacttgatggtgaagga 21 60 150768 Coding 3 1456 gggatccggccgtaggtgac 0 61 150769 Coding 3 1476 ggtttgacatccctgggtaa 3 62 150770 Coding 3 1514 catccggtatccacgctcca 20 63 150771 Coding 3 1562 gcgcatcatgatgttgtaga 2 64 150772 Coding 3 1618 agcacactctggatgtattc 9 65 150773 Coding 3 1621 tccagcacactctggatgta 19 66 150774 Coding 3 1624 tcatccagcacactctggat 43 67 150775 Coding 3 1665 atggctgctgttggtactgg 28 68 150776 Stop 3 1675 cctccctatcatggctgctg 19 69 Codon 150777 3′UTR 3 1716 ccttcgagccaccacctggg 42 70 150778 3′UTR 3 1822 cagtccaacctacccactgg 5 71 150779 3′UTR 3 1850 ggattgcaagagtcaaaaag 17 72 150780 3′UTR 3 1860 gtcagattgtggattgcaag 20 73 150781 3′UTR 3 1869 cctgagaatgtcagattgtg 24 74 150782 3′UTR 3 1923 gctgtaactaaaatccaacc 10 75 150783 3′UTR 3 1926 acagctgtaactaaaatcca 1 76 150784 3′UTR 3 1954 actattttgaaagtttccct 10 77 150785 3′UTR 3 1961 tcatttcactattttgaaag 0 78 150786 3′UTR 3 1994 taagacttgcatttatatct 24 79 150787 Intron 5 10 5506 agatgtgcaccaccatgctt 0 80 150788 Intron 5 10 7370 tgcaccaccctatattatca 9 81 150789 Intron 5 10 7447 aacatacatattaggctggt 0 82 150790 Intron: 10 8444 gagtagcttcctgaattgac 0 83 Exon Junction 150791 Intron: 10 8941 tcgttcccctctggaacaga 30 84 Exon Junction 150792 Exon: 10 9094 gggtccttacccatccagac 6 85 Intron Junction 150793 Intron 9 10 17271 ggccagcagaagatgccaca 21 86 150794 Intron: 10 25867 tttgacatccctgaaaagga 22 87 Exon Junction

[0271] As shown in Table 1, SEQ ID NOs 13, 17, 18, 19, 20, 22, 33, 34, 35, 36, 37, 39, 40, 42, 47, 51, 53, 57, 58, 66, 67, 68, 69, 70, 73, 74, 79, 84, 86 and 87 demonstrated at least 19% inhibition of human hematopoietic cell protein tyrosine kinase expression in this assay and are therefore preferred. The target sites to which these preferred sequences are complementary are herein referred to as “active sites” and are therefore preferred sites for targeting by compounds of the present invention. Example 16

[0272] Western Blot Analysis of Hematopoietic Cell Protein Tyrosine Kinase Protein Levels

[0273] Western blot analysis (immunoblot analysis) is carried out using standard methods. Cells are harvested 16-20 h after oligonucleotide treatment, washed once with PBS, suspended in Laemmli buffer (100 ul/well), boiled for 5 minutes and loaded on a 16% SDS-PAGE gel. Gels are run for 1.5 hours at 150 V, and transferred to membrane for western blotting. Appropriate primary antibody directed to hematopoietic cell protein tyrosine kinase is used, with a radiolabelled or fluorescently labeled secondary antibody directed against the primary antibody species. Bands are visualized using a PHOSPHORIMAGER™ (Molecular Dynamics, Sunnyvale Calif.).

1 87 1 20 DNA Artificial Sequence Antisense Oligonucleotide 1 tccgtcatcg ctcctcaggg 20 2 20 DNA Artificial Sequence Antisense Oligonucleotide 2 atgcattctg cccccaagga 20 3 2015 DNA Homo sapiens CDS (169)...(1686) 3 cggaggcacg gaagatgagg aagatgatca ggaggatgat gaaggtgaag agggagatga 60 agacgatgac gacgatggct ctgaggggac ctcaggggct gccgagctgg gggggcgctc 120 aagctgcgag gatccgggct gcccgcgaga cgaggagcgg gcgccagg atg ggg tcg 177 Met Gly Ser 1 atg aag tcc aag ttc ctc cag gtc gga ggc aat aca ttc tca aaa act 225 Met Lys Ser Lys Phe Leu Gln Val Gly Gly Asn Thr Phe Ser Lys Thr 5 10 15 gaa acc agc gcc agc cca cac tgt cct gtg tac gtg ccg gat ccc aca 273 Glu Thr Ser Ala Ser Pro His Cys Pro Val Tyr Val Pro Asp Pro Thr 20 25 30 35 tcc acc atc aag ccg ggg cct aat agc cac aac agc aac aca cca gga 321 Ser Thr Ile Lys Pro Gly Pro Asn Ser His Asn Ser Asn Thr Pro Gly 40 45 50 atc agg gag gca ggc tct gag gac atc atc gtg gtt gcc ctg tat gat 369 Ile Arg Glu Ala Gly Ser Glu Asp Ile Ile Val Val Ala Leu Tyr Asp 55 60 65 tac gag gcc att cac cac gaa gac ctc agc ttc cag aag ggg gac cag 417 Tyr Glu Ala Ile His His Glu Asp Leu Ser Phe Gln Lys Gly Asp Gln 70 75 80 atg gtg gtc cta gag gaa tcc ggg gag tgg tgg aag gct cga tcc ctg 465 Met Val Val Leu Glu Glu Ser Gly Glu Trp Trp Lys Ala Arg Ser Leu 85 90 95 gcc acc cgg aag gag ggc tac atc cca agc aac tat gtc gcc cgc gtt 513 Ala Thr Arg Lys Glu Gly Tyr Ile Pro Ser Asn Tyr Val Ala Arg Val 100 105 110 115 gac tct ctg gag aca gag gag tgg ttt ttc aag ggc atc agc cgg aag 561 Asp Ser Leu Glu Thr Glu Glu Trp Phe Phe Lys Gly Ile Ser Arg Lys 120 125 130 gac gca gag cgc caa ctg ctg gct ccc ggc aac atg ctg ggc tcc ttc 609 Asp Ala Glu Arg Gln Leu Leu Ala Pro Gly Asn Met Leu Gly Ser Phe 135 140 145 atg atc cgg gat agc gag acc act aaa gga agc tac tct ttg tcc gtg 657 Met Ile Arg Asp Ser Glu Thr Thr Lys Gly Ser Tyr Ser Leu Ser Val 150 155 160 cga gac tac gac cct cgg cag gga gat acc gtg aaa cat tac aag atc 705 Arg Asp Tyr Asp Pro Arg Gln Gly Asp Thr Val Lys His Tyr Lys Ile 165 170 175 cgg acc ctg gac aac ggg ggc ttc tac ata tcc ccc cga agc acc ttc 753 Arg Thr Leu Asp Asn Gly Gly Phe Tyr Ile Ser Pro Arg Ser Thr Phe 180 185 190 195 agc act ctg cag gag ctg gtg gac cac tac aag aag ggg aac gac ggg 801 Ser Thr Leu Gln Glu Leu Val Asp His Tyr Lys Lys Gly Asn Asp Gly 200 205 210 ctc tgc cag aaa ctg tcg gtg ccc tgc atg tct tcc aag ccc cag aag 849 Leu Cys Gln Lys Leu Ser Val Pro Cys Met Ser Ser Lys Pro Gln Lys 215 220 225 cct tgg gag aaa gat gcc tgg gag atc cct cgg gaa tcc ctc aag ctg 897 Pro Trp Glu Lys Asp Ala Trp Glu Ile Pro Arg Glu Ser Leu Lys Leu 230 235 240 gag aag aaa ctt gga gct ggg cag ttt ggg gaa gtc tgg atg gcc acc 945 Glu Lys Lys Leu Gly Ala Gly Gln Phe Gly Glu Val Trp Met Ala Thr 245 250 255 tac aac aag cac acc aag gtg gca gtg aag acg atg aag cca ggg agc 993 Tyr Asn Lys His Thr Lys Val Ala Val Lys Thr Met Lys Pro Gly Ser 260 265 270 275 atg tcg gtg gag gcc ttc ctg gca gag gcc aac gtg atg aaa act ctg 1041 Met Ser Val Glu Ala Phe Leu Ala Glu Ala Asn Val Met Lys Thr Leu 280 285 290 cag cat gac aag ctg gtc aaa ctt cat gcg gtg gtc acc aag gag ccc 1089 Gln His Asp Lys Leu Val Lys Leu His Ala Val Val Thr Lys Glu Pro 295 300 305 atc tac atc atc acg gag ttc atg gcc aaa gga agc ttg ctg gac ttt 1137 Ile Tyr Ile Ile Thr Glu Phe Met Ala Lys Gly Ser Leu Leu Asp Phe 310 315 320 ctg aaa agt gat gag ggc agc aag cag cca ttg cca aaa ctc att gac 1185 Leu Lys Ser Asp Glu Gly Ser Lys Gln Pro Leu Pro Lys Leu Ile Asp 325 330 335 ttc tca gcc cag att gca gaa ggc atg gcc ttc atc gag cag agg aac 1233 Phe Ser Ala Gln Ile Ala Glu Gly Met Ala Phe Ile Glu Gln Arg Asn 340 345 350 355 tac atc cac cga gac ctc cga gct gcc aac atc ttg gtc tct gca tcc 1281 Tyr Ile His Arg Asp Leu Arg Ala Ala Asn Ile Leu Val Ser Ala Ser 360 365 370 ctg gtg tgt aag att gct gac ttt ggc ctg gcc cgg gtc att gag gac 1329 Leu Val Cys Lys Ile Ala Asp Phe Gly Leu Ala Arg Val Ile Glu Asp 375 380 385 aac gag tac acg gct cgg gaa ggg gcc aag ttc ccc atc aag tgg aca 1377 Asn Glu Tyr Thr Ala Arg Glu Gly Ala Lys Phe Pro Ile Lys Trp Thr 390 395 400 gct cct gaa gcc atc aac ttt ggc tcc ttc acc atc aag tca gac gtc 1425 Ala Pro Glu Ala Ile Asn Phe Gly Ser Phe Thr Ile Lys Ser Asp Val 405 410 415 tgg tcc ttt ggt atc ctg ctg atg gag atc gtc acc tac ggc cgg atc 1473 Trp Ser Phe Gly Ile Leu Leu Met Glu Ile Val Thr Tyr Gly Arg Ile 420 425 430 435 cct tac cca ggg atg tca aac cct gaa gtg atc cga gct ctg gag cgt 1521 Pro Tyr Pro Gly Met Ser Asn Pro Glu Val Ile Arg Ala Leu Glu Arg 440 445 450 gga tac cgg atg cct cgc cca gag aac tgc cca gag gag ctc tac aac 1569 Gly Tyr Arg Met Pro Arg Pro Glu Asn Cys Pro Glu Glu Leu Tyr Asn 455 460 465 atc atg atg cgc tgc tgg aaa aac cgt ccg gag gag cgg ccg acc ttc 1617 Ile Met Met Arg Cys Trp Lys Asn Arg Pro Glu Glu Arg Pro Thr Phe 470 475 480 gaa tac atc cag agt gtg ctg gat gac ttc tac acg gcc aca gag agc 1665 Glu Tyr Ile Gln Ser Val Leu Asp Asp Phe Tyr Thr Ala Thr Glu Ser 485 490 495 cag tac caa cag cag cca tga tagggaggac cagggcaggg cagggggtgc 1716 Gln Tyr Gln Gln Gln Pro 500 505 ccaggtggtg gctcgaaggt ggctccagca ccatccgcca gggcccacac ccccttccta 1776 ctcccagaca cccaccctcg cttcagccac agtttcctca tctgtccagt gggtaggttg 1836 gactggaaaa tctctttttg actcttgcaa tccacaatct gacattctca ggaagccccc 1896 aagttgatat ttctatttcc tggaatggtt ggattttagt tacagctgtg atttggaagg 1956 gaaactttca aaatagtgaa atgaatattt aaataaaaga tataaatgca agtcttacg 2015 4 20 DNA Artificial Sequence PCR Primer 4 tttgtccgtg cgagactacg 20 5 19 DNA Artificial Sequence PCR Primer 5 ttgtccaggg tccggatct 19 6 29 DNA Artificial Sequence PCR Probe 6 ctcggcaggg agataccgtg aaacattac 29 7 19 DNA Artificial Sequence PCR Primer 7 gaaggtgaag gtcggagtc 19 8 20 DNA Artificial Sequence PCR Primer 8 gaagatggtg atgggatttc 20 9 20 DNA Artificial Sequence PCR Probe 9 caagcttccc gttctcagcc 20 10 30000 DNA Homo sapiens exon (4334)...(4437) exon 5 10 gatcttctcg cctcagcctc ccaaaatgct gggattatag gcctgaacca ctgcacctgg 60 cccatccctc atttgattca ttcgacaagc acatgctcat gactcttcaa gccctgtgcc 120 agcctaaggg gctgtggaaa caaataagat atatccctac cctcaaggag ctctccataa 180 cccatcgttc ttggctgtgg gttcttcttg tgtctagctt gactctaaaa atatacttca 240 gtcatccatc catccatcca tccattcatc catccatcca tccatccatc catccatcca 300 tcatccaaca gatacctgtt gattccctat tccagggtta gaagatgact tagatggggc 360 tccctgctgg agatgttctc tgtatggtgg atgaggttga tgagtaaaaa gatgactaca 420 ttgtggggtg gcaatacatc ccattaaaaa ccagccaatc aaaagttgac aaatgacagt 480 ccccattgtt ttgtctcttc tgcctcctct ttctagctag atggtattat gggtttggga 540 tgcttgcctg ttaaaaatga aaacgcttag gcttttccca ttataaagcc acctccttct 600 ggctgggcat ggtggctcac acctgtaatc ccagcacttc gggaggccaa ggcacgcaga 660 tcacctgagg tcaggagttc gagaccagcc tgaccaacaa ggtgtaaccc catctctact 720 aaaaatacaa aaaaaattag ctgggtgtgg tggtgcgtgc ctgtagtccc agctactcgg 780 gaggctgagg caggagaatc acttgactcc agggggcaga ggttgcagtg agctgaaata 840 tcatgccact gcactccagc ctgggggaca agagcgatac tctgtcaaaa aaaaacaatt 900 atgtcacccc ttcttagtga tcatggaact gggggctctt agctgtttct ctctccttct 960 tccaggcttt gccctgggtc atcccatgct ctgtttctcc actccagggt ctgaacactt 1020 acagaatccc tgggtcacct catgtagtcc ttgcagcaac catggaggag gcgtggctgg 1080 cattatttct caaaggcaac ataattgcta agtggaaaac gcagggtgta gacaacatga 1140 atggggggtt atcatttgca gacaaaggca aaataaccta gatggggggt tctcagacat 1200 gagcagcaac agcatcacct ggattgccgg ctaacaagtg ctttctgggc tccactgtca 1260 gattccgaat gtgcatttct aacaggttct tgggtgaggc agctgctgct gctgctgctc 1320 cagggaccca gcttgggaac cactgatcta aatacgcata tctggccagg tgtggtggct 1380 cacacctgta atcccagcac tttgggaagc cgagggaggt ggaacacttg aggtcaggag 1440 ttcaagacca gcctggccta catggtgata ccctgcctct actaaaaata caaaaattag 1500 ccaggtgtga tggcgggctc ctgtaatccc agctactcag aggctgaggc acgagatttg 1560 cttgatctgg gaggcagagg ttgcagtgag ccgagatcac gccactgcac tccagcctgg 1620 acaacagagc gagactctat ctcaaaaaat aataataaaa ataacaaatg aatacacata 1680 tgtgtccttt cagggcactc aggggtcctt gtgtctgaat caagaaactg ctaacagagg 1740 ttgcctctgg ggagcacaac tgggaccttg ggaatcaggg cgggatggaa tcttggtttc 1800 tctcattctc ccttgaaata ggcaatactt tcaaatgttt caaaatgcaa atgtggggaa 1860 gcatgcagaa gagtgaaaag tcttcttccc accctgtccc caaccagcca cttcccctcc 1920 ccagaagcaa ccagtttctc gtgagtcctc ccagatgctt cctccttata taagaaaaga 1980 catctcttcc cgcttatctc acacaagtgg tagataccac acacactgtt ccatgcctct 2040 cgttcagacc ttccatgcag caccttgttc ctgttttgtt ttgttttgtt ttgttttgtt 2100 ttttaggtgg agtttctctc ttgttgccca ggctggagtg caatggtgtg atctcggctc 2160 actgcaacct ccgcctcccg ggttcaagcg attctcctgc ctcagcctcc caagtagctg 2220 ggattacagg catgcgccac catacctagc taattttgta tttttaatag agacagggtt 2280 tctccatgtt ggtcaggctg gtctcgaact cctgaactcg tgatcctcct gccttggcct 2340 cccaaagtgc tgggattaca ggcgtgagcc actgctcccg gacacctcct tcctttttat 2400 accacagggc gtctgtcctg tagatgtcct accgtccatt taacctctgc cctatacagt 2460 ggtcacttaa gttgtttcca gtcatgtact gaagcgaatc tcctggtgta tatgtcattt 2520 ctcccttgtg caaggtctat gggataactt cctaggacca gaattgtcag ggagacagtt 2580 ggtttttttt gtttgtttgt ttgtttgttt ttgagacaga gtctcgctct gttgcccagg 2640 ctggagtgca gtggcgtgat ctcggctcac tgcaagctcc acctcccagg ttcacaccat 2700 tctcctgcct cagcctcccg agtagctggg actacaggct cctgccacca tgctcggcta 2760 attttttttt ttttttttgt atttttagtc gagacggggt ttcaccatgt tagccaggat 2820 ggtctcgaac tcctgacctc gtgatccacc cgcctcggcc tcccaaagtg ctgggattac 2880 aggtgtgagc caccgcgccc agccggggga gacagttctt agtcttacat agttgaatat 2940 tttaccatgg cacaagtcac tttacaacat gaaagcaaag aaggtagatg agcaacatag 3000 catggtgatt cagagcttgg gttctggagt tagactgcct agcttcaaat cctgcctcta 3060 caacttccca gctgtgtgac tctaggcaag tcacttgccc tctctgttcc tcaatttcat 3120 catccataaa atggggccag gagcagtggc tcatacctgt aatcccatca ctttgggagg 3180 ccaaggtgga tggatcacct gagttcagga gttcgagacc agcctggcca acatggtaaa 3240 accccgtctc tactaaaaat acaaaaatta gctaggtgta gtggtgggtg cctgtaatcc 3300 cagctgcttg ggaggctgag gcaaaataat tgcttgaacc cgagaagcag aggtttcagt 3360 gagcccagat cacaccactg cactccagcc tgggtgacag agcaagactc agtctcaaaa 3420 aaaaaaaaaa aaaaaaaaag ggggggaatg ataaaggtga caactccata gagctgttgg 3480 gtggatagca agatagatgt taacttcctc cccagttgat aacagaggaa ccaaaggccc 3540 aaagaggaag gcaacttgct caaagtcaca ctgcaggttt gtggcagagc caaggcaggc 3600 tgaggtcagg tctggggctt ttttccaact gctcctcacc ccagtgaagg tgggaatgga 3660 ttccactgct gctgcttgaa cttttccacc caaatatctc aatattcagg aagaatgaag 3720 aaaatgtccc aggatataat cctaagtata aaattctttc caatctcaca ttgtagctta 3780 gaagttcagg ccaactttat attcaactcc atatatgcgg aggaggattg gttgtaaagc 3840 taacaaaact caggcccttc acaggcttcc aaggtcccaa gaaggatctt ccccgtggtc 3900 ttgtatgctt gtgaaacctg caaaagtaag actttgacca cagctggtta agactgctgt 3960 ctgtttccac tctgtcttcc tgtccatctc cctgtccctc acagcgagca gcactgaaat 4020 gacctatcag ctttttgcac ttgttaatgc tgtattattt ttcttaaagg aagttccccc 4080 actccaaatt gcataggctt cagtctcagc aaacaggatt cacttcgggt aaaatgtcta 4140 ttttgatatc aaaagaatgg ctcctttacc ttctctcccc caaaaaatct ttgagtaaaa 4200 ctgatgctgc aggaagccag accctctgta tcctgacatt cccctgggac ctgcatggcc 4260 acaggcatcc tgtgtaggcc ggacaggact gcatgacccc aggttcacat ttgtcccctc 4320 ccttttccat caggtggttt ttcaagggca tcagccggaa ggacgcagag cgccaactgc 4380 tggctcccgg caacatgctg ggctccttca tgatccggga tagcgagacc actaaaggtg 4440 acaccagccc tccccacctt gtcctccctg ccgaggtgcc ccagctgggg ctggccacca 4500 ccctttcctt ggaaaatgcc ctgggaaagg ctgaaaaacc caaccaggtg ctgtggctgc 4560 caggtttctc ctgctcttgg ccacctgagc tggggagggt tgaggctctg tgcctggctc 4620 tgcccttctt atccaccata gctgccagct taggtcagtg gaactagtgc caggtggctt 4680 aggccctgaa aacaaagaaa catccagctg aagcttgatc ttcactgact tgttttttca 4740 tttgttttgg ttcttgtttt gttttgttct gttttttgag atggagtctc actctgtcgc 4800 caggctggag tgcagtggtg cgatctcggc tcactgcaac ctccacctcc caggtttgag 4860 cgattctcct gcctcagcct tccaagtagc tgggattaca agtgctcgcc accatgccca 4920 gctaattttt gtatttttag tagagacagg gtttcaccat gttggccagt atggtctcga 4980 tctcctgacc ttgcgatcca cccctcttgc cctcccaaag tgctgagatt acaggcgtga 5040 gccactgcgc ctggcctgtt ttgttttgtt tgagacaggg tctcactctg ttgcccaggc 5100 tggtatgcag tggcacaatc tcagctcact gcaacttctg cctcctgggc tcaaatgatt 5160 ctcccatctc agtctcccga gtagctggga ctacaggtac gtgccaccat gctgactaat 5220 cttttctttc tgtttttctt tctttctttt tagtagagat ggggttttgc catgttgcct 5280 aggctggcct cgaacttctg gactcaagca atctgcctac ctcagccttc caaagtgtca 5340 ggactacaaa gtgtcaggat tgtttttgtt ttggtttttt taaatacccg taacagacca 5400 agtaggggag gccaacacag gaggatcact taagcccaaa agttcgagac cagcctgggc 5460 aacatagtga gaccccatct gtatgaaaaa ttttaaaaat tagccaagca tggtggtgca 5520 catctgtact ccctgatact cagaagggtg aggccagatg atctcttgag tccaggagtt 5580 caaggctgca gcgagccata atggagccac tagactccag cctgggcaac agagcaagac 5640 cccatctcta aaaaaataaa acaaaatacc cattacaata gatcttatcc acaagcctca 5700 ttcctccttt cctccctcca taaggaaatg aggtaggatg aggtcgccag aagagactca 5760 agccagcctt ctctgggact ctgctgaaaa tgctccttgg aagcttttgg aagttttaat 5820 gtcaggtgac cagcttcctg gaatttctgt gctgcaaggg tggattcatg ctgattgggt 5880 gcatggatgg caagaacagg cctggaaaac atcgcgtagc tcaaactggc atcgattgag 5940 gctcattgcc tcaaaggaat gaacatcagt aggattctta tgatttcaga tttcatgtgc 6000 taagtgcacc tttactaata catttaggtt cacaactgct tgactcaaat aagccaagta 6060 tattgtataa tatgtgacct cacggtaccc tgaagcaaac agatttgggg acattgatta 6120 aaggcatgtt cctcatgtgg ccttctactt gaccctcagc tatctgaatt ggcgaagctt 6180 tcatgtggct aggataatgc tacccacaat cagtgtggca gctcagtgaa tgcctgggct 6240 ttgtctcttc ccacccaacg agccccattc aagcccccag ggggaagaaa aggagataaa 6300 aagacaaagc tgtgcacagc ccagcgcttc tcctctctag ctgtgcccag gacagctttt 6360 ggcttgggct ggtccatcct gcagacaagg gcagagaaat caaagaaacc atcacagatc 6420 tgtggggcag gaaaatgagc ctggtccagc tttcacagct ctctgagatg gggcatgttg 6480 ggaattttag ccgatttaat aaaagttgca gcatgagacc tgtgaatccc accctgctgc 6540 ttcctggatc ctgccacacc ccatccagca gcaaccaagc cagtctcgcc cctgactggg 6600 acagagtggc tgagaggggc tctggagcca gctgcctgga tttgaatccc agctgtgcca 6660 cttaccagct gtgtgactgt aggtgagtta tttcacctct ctgggcttca gtttcctcat 6720 ccgtaaatga ggatgatgat attataaaac ccttacccca tgaggttatt cattcattaa 6780 ataaataata ttataattta tatagttata attcattata atgaatatta ttcttattca 6840 ttcattgttc atctacgcag agtgctttga acttgcctgg catgtacggt aagctattat 6900 tcattcaaca gtataaactg gccaggtgag gtgactcaag cctgtaatcc cagcagtttg 6960 ggaggctgag gcatgtggat cacctgagct caggagttgg agaccagcct ggccagcatg 7020 gtgaaactcc atctctacta aaaatacaaa aattagccgg gcgtagtggc gggcgtctgt 7080 aatcccagct actcaggagg ctgaggtagg agaattgctt gaacctggga ggcagagatt 7140 gcagtgagcc aagattgcgc cactgcactc cagcctggat gacacagcga gactctgaca 7200 cacacacaca aaaaataaag tttaaacttc ccaaatccta tgacattgta ctattatcat 7260 ggtaaagaac actgagacag agggactaat aacttgccca agggcacaca gctcacaaat 7320 agcaaaacgg tggtcatgag ctgaaagact tatgtgtttc tgctctatgt gataatatag 7380 ggtggtgcaa aagtaatttc agttttttcc actacttttg aaggcaaaaa ctgcaattac 7440 ttttgcacca gcctaatatg tatgttaggt tcccattgct gctgtaacaa attaatacaa 7500 acttagtggc ttaaaacaac acccgtctat tctctaacag ttctggggat cagtagtctg 7560 acctcactgg gctcaagatg tcagcagggc tggttccttc tggaggcttc aggggagaat 7620 tcattttctt gcctttttta gtttccagag gctacagcat tccttggctc atagtccctt 7680 cctgacatct gtccaagctc ttgtttccat cttcacctct tccactttga ccttcctacc 7740 tccttctaac aagaactcaa gggattacac tggggctacc tggatcatct ggaataatct 7800 ccccgtctcc agatccttaa cttaatcaca tctctaaagt accttttacc atgtaaggta 7860 acatattccc aggttccagg gtttagggca tgactatctt gagggaccac tattcagcct 7920 accacagcat gttcacattt caataactgg actggatttc tgggtttttt tccagaaaag 7980 tcatagcctg agtttttatg aaaaagtaaa aagtatacta tggtctcttg gctttttgta 8040 gggtagatga tagaaagatg gaacaataga tcagaaataa tgaagatgat gatgatgata 8100 gccaacattt gcagagtgtt cagcttccaa gtagtttaca ggcattactt cttttagccg 8160 tcaggcaata ggatcaggta gggaggcgtg agaactattc ccattttaca gatgagaaaa 8220 ctgaggcata gagaggtgac atagtcacat ggccaaggtc tcacgggtgg atgtggtaga 8280 gcctggatga gagcccagga tgcctggctc ccacagccca ctcagaccct cgggcacttc 8340 tgcccaggtg tcaggacggt gccagcggta gccttacagg gtgtcagagt gctaatgcaa 8400 ggtggcaggc ctccaagatg ccattctgag gggtttctct ttggtcaatt caggaagcta 8460 ctctttgtcc gtgcgagact acgaccctcg gcagggagat accgtgaaac attacaagat 8520 ccggaccctg gacaacgggg gcttctacat atccccccga agcaccttca gcactctgca 8580 ggagctggtg gaccactaca agagtgagtc ccaccccagg ggtgacatcc ccaccacgat 8640 gggcccacag actcctagtc acggatgcac tgtggcccct gagacctgct gtgtccttct 8700 tggccatccc ctagacagat agttgctttg gatgcttctg aaggcttagg actgttgagc 8760 aggagggtga ggtggccaag atgtagaggt ggcaccccgt cacactctgc ttgcttggga 8820 atgtctctga tggtggcaac caggtggaac actggagaga tccagtggac caggtagggc 8880 ggcctccaag gagcaacctc tggctggctc ggtgcttgtt gctctcaatt gaccagggac 8940 tctgttccag aggggaacga cgggctctgc cagaaactgt cggtgccctg catgtcttcc 9000 aagccccaga agccttggga gaaagatgcc tgggagatcc ctcgggaatc cctcaagctg 9060 gagaagaaac ttggagctgg gcagtttggg gaagtctgga tgggtaagga cccagggcca 9120 cagcccacag ggccagaggg tggaggggag agggaggcca cttgcttcca ggaacacctt 9180 atggcaaagc gggaatgcta cccaaggcag agggggagat ttaaataata gccataaaga 9240 agcagttccc tgatagcaaa ccaaattgtc ttgctgtgca aacactgatt tgcctttgag 9300 accagtcctg tagtggtcaa aaacttcctt ctgggaagca ggtgtcatgg atgaggaatc 9360 cctccctcat acggagtggg gactgcctaa cagtttggga ttgagataac cagagacctt 9420 ttcagatgat gaaaattaag aatggggaaa tgcagcttgg agatttccag gcaactgatg 9480 aacaggttat tctgagcacc tgctgtgtgc ccagcactgt tagggtcttg tgggaaaatc 9540 agaaaggcac atctcacacc tgctgatttt ccccaagaac ttaagaacaa cactgcctgc 9600 tttgcagggc tgtggggtag atgcagtgcc agcccagtgt ggggcagcct gctgtgttaa 9660 tacgttccaa atgggagcgt tccaaatggg agcgaagaca acttacaggg atgcaaacaa 9720 ctcagccaga taaaataagt ttaaaatcca tgtatttcga ctgtatttat tgcgattctg 9780 ctgcatgcaa ggccgggcac agtggctcac gcctgtaatc ccagcacttt gggaggccga 9840 ggcaagtgga tcaatcaagg tcagcagttc gagaaaaacc tggatagtat agtgaaatcc 9900 cgtctctacg aaaaaataca acaattagcc aggcgtggtg gtgggagcct gtaatcccac 9960 ctactcggga ggctaaggca ggagaatcgt ttgaacccag gaggtggaag ttgcagggaa 10020 ccgagatcgc accactgcac tccagcctgg gagacagagt gagactctgt ctaaaaaata 10080 ataataaaat taaaaagaat ttgacaaaaa agaaaatatg gagaggaagg taagacagat 10140 ctgagtggtg agatttgaaa gccaaaaata tcatataaga cgctagactc ctactacagg 10200 aagcccacgg ttctggattg gagcttcctg gaagccaagg caaaatggaa acccaagcaa 10260 ttataaaatt gacaagaccc accaaatgaa gcagggtggg gtgaggggag ggaacagcat 10320 gtgccaaatc cctgtggtgg gaggtgagtt gggtgcttga gggactgagt gacctgcagg 10380 gtgactggca cataaaaggc aaggggagtt tagtggctga tgaggctaga ggggtggacg 10440 aggctgggtc atgtagggcc tgggggtcat agtaagtctg gcatttattt aagagcagtg 10500 ttaagattaa agtgggcggt gtatgtgtgt gacataacct gagtagtgtt ttaaagctat 10560 ttttatttgt ttgggttttt tgtttgtttg tttgtttgag acagagtctc gctctgtcac 10620 ccaggctgga gtgcagtggc tcaatcttgg ctcactgcaa gctccgtctc ctgggttcac 10680 accattctcc tgcctcagcc tccccagtag ctgggactac aggcgcccac aactgcgcct 10740 ggctaatttt ttgtattttt agtagagacg gggtttcacc gtgttagcca ggatggtctc 10800 gatctcctga ccttgtgatc cgcccacctc ggccccccaa agtgctgaga ttacaggcgt 10860 gagccactta gagctatttt taaatccttg caacagcact tcaaaggcaa agcttaccat 10920 ttccacttta cagatgagga agctgaggaa gccacggctc agagacgtta agccacttgc 10980 cctagtgtgc acagctggga agtggtgaac ccgcctttca acccacagtt gtctgaggcc 11040 taagcccatg atttcgcttc cctctctgag agttgagatg agcaggaaag actttctgga 11100 ggaggcgggt ctgcagctgg gccttctagg gtggtacggg agaccagtgg gctctgacca 11160 ccttccctgc tctctatccc cctccagcca cctacaacaa gcacaccaag gtggcagtga 11220 agacgatgaa gccagggagc atgtcggtgg aggccttcct ggcagaggcc aacgtgatga 11280 aaactctgca gcatgacaag ctggtcaaac ttcatgcggt ggtcaccaag gagcccatct 11340 acatcatcac ggagttcatg gccaaaggtg ctgcgtgctg gggctggggg tgcaggctgt 11400 ggcctatact ggtcaattgc gggcccaagg gtggcttgga catggttctt gcccttgaga 11460 tggccccaat ctggccagga gctcttccaa caagtactca ttgagaatct aatgtggaac 11520 aatccagccc tcctggttag tggggtgaaa tcatgttaag gggtcaccaa ggggaaggga 11580 gaacaagggg ctaccaggag aagggaatgg ggccagaata ctcctgggca atgggagaag 11640 gggcttatgg ttcacagtga gccttagagg ccagggtgtg gcatgggtgg tgggggtgcc 11700 actctcccgc atcagccacc ttccctgtac ttgccaaagc cctgggagag ggagctggca 11760 aagcagcagt tctgccccca cccccgccct gccacaactc aggatttctt ggggaatttt 11820 tttaggccac tgtttcacaa ccattttcaa cccctgccat tttttgtttg tttgtttttt 11880 agggacagga acttgctctg ttactcaggc tggagtgcag aggtgcaatc ataactcctg 11940 ggctcaagtg atcctcccac cccagccccc cgagtggctg ggaccacagg cccatgccac 12000 cacactcagc taattttatt tatttattta catatttatt tttagagaca gggttgccct 12060 ctgcctaccc aggctggagt gcagtggcgt gatcatagtt cactgtagcc tcaaactctc 12120 aggctccagg atcctcccga cttagtctcc ccagtagctg gcactacagg catgcactac 12180 cacacccagc taatttctaa aaaaattttt tttttttttg agacagagtc tcactctgtt 12240 tcccaggctg gagtgcagtg gcacaatctc ggctcaatgc aagctccacc taccaggttc 12300 acgccattct cctgcctcag cctcccaagt agctgggact acaggtgcct gccaccatgc 12360 ctggccaatt tttttgtatt tttagtagag acggtgtttc accgtgttag ccaggatggt 12420 ctcaatctcc tgaccttgtg atccgcccgc ctcagcctcc caccatgctg gaattacagg 12480 cgtgagcaac tgcgcccagc ttctaaaatt tttttctaga gacaaggtct cgccatcttg 12540 ccccagctgg tctcaaactc ctgggttcaa ctgatcctcc caaagctttg ggattatagg 12600 catgaaccac tgagcctggc ctaacatata tatttgtaaa tttcttctat agatggggtc 12660 ttgcgatgtt gcccaggctg gtctcaaact cttggcctca ggtgatcctc tcacctcggt 12720 ctcctaaagt gttggaatta caggagtgag cctcgtgcct agccactctg cccatttttt 12780 gataaacaga atcatctcat gcaatcccat ttagtgcgat ttgaaacctc aagccttttt 12840 cattttaact atgcaattat gccagtcctg tgaaggcatg atcccagcca tccaggctca 12900 ggggctgtct cagtcacaga atccatctag caatcaaaaa gtcacttcac taaaactcaa 12960 ttctctttct caaacactag gaattgcaaa caaatattcg tatttaaatc tactactatg 13020 aaaaatcttc accacacact aaagtactag attggtgcaa aagtaattgt ggtttttgcc 13080 attaaatagt aaaagtagta aatgttcctc ccctctcccc catataggaa gcttgctgga 13140 ctttctgaaa agtgatgagg gcagcaagca gccattgcca aaactcattg acttctcagc 13200 ccaggtgaga gcctaacgag gaaacgggga agggaaacag gaattcgatt tttttacttg 13260 ccaaatattt actgaccaca tactatgatg atagcagtaa taataatggg taaaatgtat 13320 tgagagctca gtataaaact atgttttttg catatatttt attatacatg tactcattca 13380 tttaatcatc ctataagctt tataggctgg gatttttgtt atctattttg gtataacaaa 13440 ccatccaagt cctagtagct tgaaacaaca gcaattgtta tttctcatga tcctgtgggt 13500 tgcctgggtt cagctgggtg gttcttctgc tcgtcatggt aaagtgaggt gcagatgttg 13560 gcacttgccc aggctagaat gtccaagaca tggctcagcc tccagggtct ctccacatag 13620 cccctcacca cccaatcacc cagcctgagc ttcttcacgg cgcagcagct gggttccaag 13680 acagagctgg accaggggcc aagccttcat gagcaggctc tcattaagcc tctgcctgca 13740 tcaggcttgc taatggccca ttggccaagt cacatagcca tgcccagaat cagtgtggga 13800 ggggactgac caaggacaca aatcccaggg accccctcaa tgtaacagtc tggccacaga 13860 gtaggtaatt atcatcccat tttacagaat aggaaattga agcatagagc agaagtaaag 13920 tacagatgtg gaaactgagc cccagtgtgg ttaagtggct tgcacaagtt actgtgctaa 13980 ttatggggga tatagcagtg aacaaaatga aaatgttcct gtcctaatag agttcacaat 14040 ccaggtggga agatgagtat taaataacca aatctcttag agaccatgac ccaagtggtc 14100 ctggctgagt caaaagagca cagtatctaa caaagtaaat aatgttcaca aatcgcaaaa 14160 acactgctga aaacctaatt ttctttctca tgttccccac gccccttgca gctcctctca 14220 cccccagcct aagcagtttt ttcacttctg tcctctctca tgctctctct gatgtctggg 14280 aaaacagagt gtaaggacgg ggtggtatta gagtgcatag ctagagcatt tagcctggtc 14340 caggagcaat cagagaatgc ttcctggagg aagtggcctc taggccgagc ctgaaggatg 14400 aatagaagtt cagtagatga agagaaaagg taaaggtctt ttagacaaaa gaaacagcct 14460 gtgcaaaagt aggtgaagga gttcagccta ctcagcagga gcccagggat agtgggagtt 14520 gagtgagacc ctgcctgggc ctcagctggg cctgctggag atgccaaggg cagggctcat 14580 ttgagtatgc aaattcaggg gcccagagga caccacaaag tgtaacaaaa gactctactt 14640 tcagagcctg gaatgccaga ggcatatgga aatgtgtttt cactcctatg ggccaggtcc 14700 tctgggagac aatagactgg tctgttgcta aattatcatc ttcaaactag cagaagccct 14760 gctgggcagc agtcaccgac cagggcaaga gccactctgc ccgtttcaca gaggggaaaa 14820 caaaccaagg gaggaaaaga ggttctgggc cttcatctgt ccagaagcag aggtagattc 14880 agagcccagg gacagaaagg agcccacctg gggctttggt cttcacctcc agactcagag 14940 aggcagcttg gagcagcagg tggagaactg gaccacacat gtggggtttc tgtagtcaca 15000 gctttgtggg tgacatgaaa tgttattcag tagctgcata tatacaaaca ggtcaaaaca 15060 gagctgctct gactgaagca gggtgggggg cttatctgtg gcctttcttt tgtctccccc 15120 acccccatat aaccttgagg catccatagg attcagttgg aagagctcta caggtccttc 15180 cagctctgat gctgtgactc cctgatactc tttggaagca aacccaaggg tgcccaacct 15240 catggcaccc tatctggggg tcatgaaatc tcaccgcctt tatcaacccg cagtgcttac 15300 acctgggccc aataaaccta ctcgttattc attcagtcag cagaccctgg agaagcaaca 15360 ctattagcat ctgggcttag gagtcacaca gagttttgtt ttgatctcag ctctgcctgt 15420 gtagcctcaa gcaagttgct taacctctct gagtgccact ttcccccact gggagcactg 15480 ggagccactc tttaaataaa tacttaacta tgtgccaaac actctactaa gcccttgatg 15540 taggcttagg ggattcatct tcacatgacc ccttggaacc aggtgctatt acagagaaga 15600 aaagtgaggt acagagagat gacacaactt gcttgacatc acagagctgc agcgctcaag 15660 ctgagttggt ccagctccag agccatttag ctattaccct ctgctgtctc ctaagtgggg 15720 tgtcatccct gccccatcga gctcctgtga aaatcagtag catatgagca tctgccagtg 15780 agcatcaaac agtggtaact accagcatta gtccttgctc cagaagaaaa gcaaggcaaa 15840 aaagctgggc caagtaacag gtaagtgcgt ggaccccaag cagcgctttt ggagctccag 15900 ccctggctcc gcaacttgca agctgtgtaa gctggggcca cttacctatt tctctgggct 15960 tcagttttct tatctgtgga aatggggctg ataacaaaag tgcctcctcc aaagcacatg 16020 gtaaatgtca cataagtgtt taagtatcat cttataaata agctatgatg ccttccatta 16080 gcatcataac ttttgttaac tgttcatcta aggactcata aatttcccac actcccaggg 16140 ccaagatgct gtctcactcc accctggcaa cctcatcccc atttcgtccc caccccccac 16200 tattctaaac aaaatcagag tctcttccaa gtttttactg aaaaatttgg gtctctgggt 16260 ctcccttggg catgacagct caggcctgta atcccagcac tttgggaagc tgaagcagga 16320 ggatccttta agcccagcct gggccacata gtgggacctc ttctctatta aaaaaaaaaa 16380 aaattctttt taaatttaat ctggcatagt ggcatgcacc tatagtacca gctgcttggg 16440 aagctgaggt gggaagactg cttgagccca ggaggcacag gttgcagtaa gctgtgatcc 16500 caccactgta ctccgtgaca gagcaaggcc ctgtctcaaa agaaaaaaaa aaagaagaaa 16560 gaaaagaaaa aagcaaagca tgggtctcca ttctaactgc ctcgggtgcc ccctgctgtc 16620 caccccttgc aagtgcgcca cccacttgcc tcagaccttg agaagccggc cggtggtgct 16680 ttgattgttc tgtctagtca gacgccctca cttccagaat aatttcatca gactgcaccc 16740 agctgcagtc tgccggagca ctggagtgct gggttattta gaggcagcag gatgcactgg 16800 attgggagtc ctcagactgg tttgagcctg acattcagaa ttttcctggt ggtgtgatct 16860 ggaacaagtg gttccatgtc tgtaaaacag agattatgat cattcctgcc tcaaagagct 16920 caagcccagt ttgtaaacca aaagtgctgc tttctgggca tctgagggtt catcttcaac 16980 cgcttttgtc caaacccttg taagtaaaaa tgtctgcaag atataatccc tgtgttttca 17040 tcagaggctt ctagggctcc tggtgtgaat aagaatcctc cacgcagtct gttagtcact 17100 cagcagccat ggtgatcttt aaatgtacat cagaacatgt cacgctcctg ctcgaaggcc 17160 tctaatatct ccccaacacg ctcagaataa aatccaccct cctctcctga cctacaaggc 17220 agttcatgat tggcggcctc cctctcaact tcaactctcc ccactctctc tgtggcatct 17280 tctgctggcc acactgacct ctgtgctgtt ccatgaacac ccaagctctt acctacctcc 17340 acgcctttgc atctcatgtt ctctctgcct agaatattct tatgcgacac acttattatt 17400 atcatcattc agatctttgc taaaatctca ccccctcaaa gcaggtttcc ctgaacgccc 17460 aatccaaaaa agctctctac aggtcatatt ttgttacttt gttttatctt ttttttcttt 17520 ttgagacaga gtcttgctct gtcgcccagg ctggaggaca gtggcacgat ctcggctcac 17580 tgcagcctct gcctcctggg tccaagcaat tctcgtgcct caacctcctg agcagatggg 17640 attacaggcg tgcaccacca tgctcatctt ctttttgtat ttttagtaga gacggggttt 17700 cgccatgttg gccaggctgg tctcgaactc ctggcctcaa gtgatccgcc cacctcggcc 17760 tcccaaagtg ctgggattac aagtgtaagc caccatgccc ggcctgtttt atcttttctt 17820 tatggtactt accacctgca ggggctttgc cgggctcatc acctgttcaa gcaacatgtc 17880 tggcacccac aagacactca gtggatttct gttgagtaaa taagtgaatt ttccctaccc 17940 aggctggggc atgaggaaga tatgagaggt atagcagaat atgacatgaa cctgggttgt 18000 ccccagaaag agagttgaag gtgaaagctc ttcatagtat cctagggttc gtgtgtgtgt 18060 gtgtgtgtgt gtgtgtgtgt gtgcatgtgc acgtgtgtgt gtatgtgtgt tcctggaaga 18120 ataggtcctg gagaaatagt cccattgctt tttccctgag aacatttcaa agtgctctct 18180 ggaagtcttg gaattctaga gaatccccca aactggccca ggcctcctta gggatccccc 18240 taacctgaat gggttgatgg aggaatgcca ccctgagccc tggggccctc ccgacacaaa 18300 agggagggct ggtgcagaca tttcgcattt tcttcacttg aacacctctc tgctgctttt 18360 gggtggggcc atcttggcgt aggccaggtc tgaggacaaa ggtgtctctg tttggggtgc 18420 agattgcaga aggcatggcc ttcatcgagc agaggaacta catccaccga gacctccgag 18480 ctgccaacat cttggtctct gcatccctgg tgtgtaagat tgctgacttt ggcctggccc 18540 gggtcattga ggacaacgag tacacggctc gggaaggtag ggaacgctgc caagcagccc 18600 cacgttgccc atttggatgc ttgtgagtgt tgagagttga tacttgtgag agcgattggt 18660 aaaatgcaag ggactgcccc agtactagct gtgcattctt gagcttggtg gatccttctg 18720 gataatgtcc tgaacttcag agtctcactc agagattttg aggagatttt agatcagatt 18780 gagaagtact gatagatttt agagggagtg ggcaaatata tgtcgaaatt aagggtaaga 18840 gcagctttgt gcataacaga caaaaatggg gagggtatcc aaatgtccat agcaggagga 18900 tggattgtgg tatattcaca caatataata ccacgcagtg atgaaaaagc acaaactggc 18960 caggctcagt ggctcacgcc tgtaatccca gcactttagg aggccaagac tggaggactg 19020 cttgagccca gaagctcaag accagcctgg gcaacacagg aagacctagt ctctacaaaa 19080 atttaagaaa ttagccaggc atggtggcac atgcctgtat gcctgtagtt gtggctactc 19140 aggaggttag ggtgagagga tcacttgagt ctaggaagct gaagctgcag taagccatga 19200 tcatgccact gcacccagcc tggtggacag agcaagatct tgtcaaaaga aaagaaaaga 19260 aaagaaaaga aagaaagaaa gaaagaaaga aagaaagaaa gaaagaaaga aagaaagaaa 19320 gaaggaaaga aagaaagaga gagaaagaga aagaaagaaa gaaagaaaga aagaaagaaa 19380 gaaagaaaga aagaaagaaa gaaagaaaga aaagaaagaa agaggcacaa gccaatgcta 19440 aatgcaccaa aatgggtaac tctcacaggt ataatatcaa aatgaaagaa attagaccaa 19500 aaaaaaagag tagatgccac ttggtttcgt ttttgtgaaa ttctaaaaga gacaaaacat 19560 gtaattggac attcatggca gcattcttcc taatagccaa aaaatggaaa caacactctt 19620 taatgtccat caattgatga acagacgaac aaaatgtgat atatccatac aatggaatat 19680 tatttggcca taaaatggaa tgaagtacta cgccaggcta gaacacagat gacccttaaa 19740 aacattttgt taaaggaaag ccaacatgaa gaccacatgt tgtataattc cccttctatg 19800 aaatgtccag aagaggcaat cttttttttt tctttgagat ggagtcttgc tgtcacccag 19860 gctagagtgc agtggctcaa tctcagctca ctgcaacctc tgcctcccag gttcaagcga 19920 ttcttgtgcc tcagccttct gagtagctgg gattacaggc gcacaccacc atacccagct 19980 aatttttgta tttttagtag ataacagggt ttcaccatgt tggccaggct gaactcaaac 20040 tcctgacctc aagtgatccg cccgccttgg cctcccaaac tgctgggatt acaggtgtga 20100 gccaccatgc ccggcccaga acagacaaat ctaaagagac agaaagtaga ttattggtgc 20160 ctacagctgg tggtggggag ttgggagaaa tgaggagtga cttctgtggg ttttttgcag 20220 ggaaatgtga tgaaagtatt ctaaaatcca caactttgta aatattctga aagccacgga 20280 attatacact ttaaatgggt gaaatgtatg gtctgtgaat tctatctcga taaagctgtt 20340 aaagaaagaa acaggcaaaa tttatttata gcactagagg tcagaattgc agtcaccttt 20400 agtttctgtt agcctaatat ttatttattt atttatttat ttatttattt atttatttat 20460 ttattttgag acggagtctc gctctgctgc ccaggctgga gtgcattggc gccatctcag 20520 ctcactgcaa actccacctc ctgggtttaa gtgattgtcc tgcctcagcc tcccaagcag 20580 ctgggattac aagcatgtgc catcatgccc agctagtttt tgtattttta gtagagacag 20640 ggtttcacca tgttggccag gctggtctcg aactgatgac ctcaagtgat tcacccacct 20700 gggcctcccg aagtgctggg attacagatg cgagccactg tgccagtcct atttattttt 20760 ttaaagagac gggtgcggcc gggcacagtg gctcacacct gtaataccag cactttggga 20820 ggccaaggca ggcggatcac aaggtcagga gtttgagacc agcctggcca atatggtgaa 20880 accctgtctc tactaaagat acaaaaatta gctgggcgtg gtggcaggtg cctgtagtcc 20940 cagctactcg ggaggctgag gcaggagaat catttgaacc cgggaggcag aggttgcagc 21000 aatgagccga gattgtgcca ttgcactcca gcctgggtga tagagcgaga ctccgtctca 21060 aaaaaaaaaa aaaaaaaaaa agataggtgc ttgctctgtt gcccaggctg tagtggaggg 21120 gtgagatcat agctcactgt agcctccaac tcttgggctc aagcaatctt ccagcctcag 21180 cctcctgagt acctgaaact acagatacgt gctaccatgc ccagctaatt ttttaattat 21240 ttgtagagat agtgtctcac tgtgttgccc aggctggtct caaactcctg gacttacgtg 21300 atcctcctgc ctcaggctct gaaagtgcta ggattacagg catgagccac tatgcacagg 21360 ctgcagtcac cttaagtaag ggggtattaa ctggaaggac gcagaaagga gcgttctgaa 21420 atgctgaaaa tgttctacag cccaatctga tggtgattac aagggtatat atatatatat 21480 aaagctgcag caaaatggat attaaagatt tgtgcatatt atttcatgta cgttataact 21540 cgattaaaaa aaatttagac cgggcacagt ggctcatgac tataatccta gcactttggg 21600 aggccaaaat gggcagattg cttgagccca ggagttcaag accagcctgg gcaatatagc 21660 aagaccccat ctctacaaaa aatttaaaaa taagtcaggc gtggtggtgt gagcctgtgg 21720 tccctgctac tcaggaggct gaggcgggag aatcgcttga gcccaggagg ttgaggctgc 21780 agtgagccaa gatcatgtca ctgcactcca gcctgtgtaa cagagcaaga ctttgtctca 21840 aaaaagtaaa taaatagggc cgggcacgtt ggctcatgcc tgtaattcca gcactttggg 21900 aggctgaggt gggaggatca cgaggtcagg agatcgagac catcctggct aacacggtga 21960 aaccccatct ctactaaaaa tacaaaaaat tagccaggcg tggtggcggg cacctgtagt 22020 cccagctact tgggagactg aggcaggaga atggcgtgaa agccgggagg cggaacttgc 22080 agtgagctga gatgacacca ctgcactcca gcctgggcaa acagagcgag accctgtctc 22140 aaaacataaa taaataaata aataaataaa tgtaatgact aaaggaataa aagtagaatg 22200 tataatttct aaaccagaag aagataagca ggaaatcaag aaaagtctgt agatccaaag 22260 gaggaaggga gaaaacatat acacacacac acactctcac acacacaaac acacacatag 22320 aacattttca aaacttgacc atgtactcag tcataaagca ggtctcaaca aattccaaag 22380 aacatatatt ctatagacca tgttcaccaa ccatgatata attaaactaa acacttttta 22440 aaaaaggata actatgccag gtgcggtggc tcacacctat aatcccagtg ctttaggagg 22500 ccaagatggg aggatcactt gagcccagga gttttgagaa caggctgggt aacataataa 22560 aacactgtct ctacaaattt ttctattttt ttatatttta ttttatttta ttttatttta 22620 tttttgagac ggagtctgac tctatcatcc aggctggagt gcagtggtgt gatctcggtt 22680 cactgcaacc tccatcccct gggttcaagt gattctcctg tctcagcctg tagctggaac 22740 tacaggcacc tgccaccatg cccagctaat tttgtatttt tagtagagat ggagttggcc 22800 aggctggtct cgaattcctg acctcaggtg atcctcctcc ttggtctccc aaagtgctgg 22860 gattacaggc acaagccacc atacctggcc aaaaaaattt ttttaattag cttggcataa 22920 tggggcacac ctgtaacccc aggggcttga gaggctgagg caggaggata gcttgaggtc 22980 aggagttcga ggcttcagtg aactatgatt gtgccactgc gctccagcct gggcactctg 23040 tctctaaaag aaaaaaaaaa tgaaaaggct aactaaaccc atgtcagact aggtgggagg 23100 aagggcgggt aaagggagag acacatagtg actggtggga acctcatggg ctgagagcca 23160 gaatcctccc ttttcccatc gcccaggatg agaggactga ggcatcagct gcaacctgga 23220 ctcaaggccc cctgaagtcc ttctgtcccc aaagacctgt gacctctggg attccactct 23280 tcggagttgc agttaactgg ggtatcagct gaatcaacga ggaggattct agagtgaact 23340 tccacaccat accccaggcc cctaagccca ctcctccttg tttagccatc tgtcctcagg 23400 atggatgtcc cttgcttcca cagggaggcc acgtatcagg gaaattgcag gtctgcaggg 23460 gcagatgttg gcagctcttg cccttgcctg ttcccccacc ttagcagagc caaccctcac 23520 tactccccag ccttccccga ctctgctctg ttcaaccctg caggggccaa gttccccatc 23580 aagtggacag ctcctgaagc catcaacttt ggctccttca ccatcaagtc agacgtctgg 23640 tcctttggta tcctgctgat ggagatcgtc acctacggcc ggatccctta cccaggtagg 23700 gaaggggcat cagctcaggg ctgctaccag ggcccagtct ggcaatgggc tcatctcaac 23760 aacatgtcca ttcaaactga gttcttgatc ctcaccccca accttccctc acctttcctg 23820 tcttagttaa aggcacctcc atccatctaa tgtcttaagc ctgaaatctg ggggcttcct 23880 tggcccttcc ttctctctca ctcctatgac tttttttttt tttttttttt tttttgagac 23940 ggagtctccc tctgtcaccc aggctggagt gcagtgacgt gatctcggct cactgcaacc 24000 tccgcctccc aggttcaagc gattctcctg cctcagcctc ctgagtaact gggattacaa 24060 gcatccacca ccatgcctgg ctaatttttg tatttttagt agagacgggg tttcaccatg 24120 ttggccaggc tggtctcgaa ctgctgacct taggtgatgc gcctgcctcg gcctcccaaa 24180 gtgctgggat tacaggcgtg agccactgtg cctggcctca cccctatgac atctgagcag 24240 tcacagggtt ttggccactc gactccaaaa catatcccaa gtctcaccac tttgaacccc 24300 acagtctcca ctgcatccag gccagcgtca tctcccatag atggtgcagc ggcatcctca 24360 tcagtcttac tgctttctcc ctcctcgtcc tacagcctat tctccacttg cagccagaag 24420 gataattcta aactttaaat cagatcttgt cctttctcca cctttttttt tttttttaag 24480 acaaggtctc actctgtcac tgaggctgta gtgcagtggt gtaatcatag ctcatggcag 24540 cctcgacttc ctaggctcaa atgatcctcc cgcttcagcc tcccgagtat ctgggaccat 24600 aggcacatgc caccatgtct ggctattttt tattttttta atttttttgt agagacttgg 24660 tctcactacg ttgtgcagcc tggtctctaa cttccaggct caaacgatcc tccagccttg 24720 gcctcccaaa atgctgggat tacagacaca caccaccatg cccagctaat tctttaaatt 24780 ttttgagaga caaggtattg ctatgttgcc gggctggtga tttccatttt taagcgatgc 24840 tttcagcatg gagagtgaat gggagggaaa gggaacaggg tggcagccag tgaggaggcc 24900 acagcagtgg cccaggcaga ggtgatgatg gtctggacag ggtggtggca ttcgtgactg 24960 gcatacgttg atgaactggt gctacgtttc aaaaggagaa aagatctgac ttgctgactt 25020 aggaggtgag agagagagaa taaaggatga ttaccctggc tttgcaccac agggtgggta 25080 atggtctagg gatagaaatt ggagagctct gttttagctc tgctaaattt gagttgactt 25140 aaatatagag acatccaagt aaaggaagca cttgagttca tgagtttgga gtttgagact 25200 aataatataa aattggggat cacagacatt gaatggctat tcttatgaat agctaataga 25260 aacttgaact gaacaaaaaa atggtcccac ccataggtta acattgaatc tggccacctg 25320 aatgttttgt cttgagggtg cactagtcaa aaccaggcaa cacacaatag acgctgaatc 25380 cattaggatg tgttccacag caagcaacaa aataacagac aaagagtaac tgaaatagaa 25440 gcaatctatt actcccaatc ttccattggt gactggttag ttcagcaact cagcagctgt 25500 caggactctg ggttcctgtc tctatgatgg tcttctccat gttgtcagct ccaagtatca 25560 taagtatctc acagtgttca aaggaagaga tgaagggtgc gttctccaaa gactctcctc 25620 taagcgggag gaaaaacctt tccatcactt tcccagcaga cctccccatc agctcccatt 25680 ggcccaaact gggtcccagg cccatgtcct agctgcaagt gaagctgagg gtggaagtct 25740 gtctttcaca gtggaagggg ctcagcttgc aaggtgaggt ggggagtgat gcctgctggg 25800 gaggccacag ggcctgccac ccctgggctc tcatttccca actgcttccg tttctaattc 25860 cacggctcct tttcagggat gtcaaaccct gaagtgatcc gagctctgga gcgtggatac 25920 cggatgcctc gcccagagaa ctgcccagag gagctctaca acatcatgat gcgctgctgg 25980 aaaaaccgtc cggaggagcg gccgaccttc gaatacatcc agagtgtgct ggatgacttc 26040 tacacggcca cagagagcca gtaccaacag cagccatgat agggaggacc agggcagggc 26100 cagggggtgc ccaggtggtg gctgcaaggt ggctccagca ccatccgcca gggcccacac 26160 ccccttccta ctcccagaca cccaccctcg cttcagccac agtttcctca tctgtccagt 26220 gggtaggttg gactggaaaa tctctttttg actcttgcaa tccacaatct gacattctca 26280 ggaagccccc aagttgatat ttctatttcc tggaatggtt ggattttagt tacagctgtg 26340 atttggaagg gaaactttca aaatagtgaa atgaatattt aaataaaaga tataaatgcc 26400 aaagtcttta ccaaaacgtt ggttttcctg tccttccaat tcctgaatat ctatttgcct 26460 tcttgctgta tgacaagtca gaaatggtga aggactctcc cggggaccag aaatacaaag 26520 acaagtgggg ttcagactgg gtgctgtggc tcccacctat aataccagtg ctttgggaga 26580 ccgaggagcg ggggattgct tgagcccagg aggtcgaggc cacagtgagc tatgatcgtg 26640 ccactgcact ctagcctgag cgacacagtg agaccctgtt taaaaaaaaa aaaaaaagat 26700 gaagaagaag aaagaaagga aaggaaagaa aattggggtt caatgcttga ggttttctaa 26760 ctgccctaaa atagttactg gctatattag tttcctcttg ctcctgtaac aaattaccac 26820 atatctggta gcttaagaca acaaaactgc ataacattac ttggccgggc ataatggctc 26880 atgcctatag ttccagcatt ttgggagact gaggtgggtg atcacttgag atcaggagtt 26940 cgagaccagc ctggccaaca tggtgaaacc ccgtctctac taaaaataca aaaattagcc 27000 aggcatggtg gtgggcgcct gtaatcctag ctactggaga ggatgaggca ggagaattgc 27060 ttgaacccgg gaggtggagg ttgcagtgag ccgagattgt accactgcac tccagcctgg 27120 gcaagacagc gagaccctgt ctcaatacat acatacatac atacatacat gtataacctt 27180 actgttccag aaaagcaaga ccctgtctca atcaatcaat caatcaatca gtcaatacat 27240 gtataacctt actgttccag aagtcagagg gactgaaatg ggttggcagg gctgcattct 27300 ttttggaggc tctaggggat aatttgtttc cttgcctttc ccagtttcta gaggctgctc 27360 ctattccttc actcatcagc ccctttcgtt cattactcca aactttgctt tcatcttcat 27420 atctcctctg agtcttcttc ccctctttta tttgtaagaa ctccttggac ccacctggat 27480 aattcagaat aatcttctca tctcaggatt cttaatcacc tttgcaaagt cccttttgcc 27540 atgtgaggta acattttcac acgctctgag ggttaggaca tgaacatctt tcgacggggg 27600 gcacttttct gccttctcca ctggtatcca gatgctggat gggttttgcc tccaaggaga 27660 tgggtcttcc aggatgacag gaatggtttc tcatgatctg ggaccctgac tttcctgtta 27720 ggccacattg ctataagagc tggtcagttt acagctcccc agagctgggg gctgcctgca 27780 gacctgacgt ttcccatggg tcaagcagcc atcatacttg tcgaagtggt atttgccatt 27840 gcaggaatcc tggtctggag atatggctgc tgagaggtgt ctagtaccct acaggggaag 27900 ctctcagtgg aggggtggga gacctgcgta ggaagcagag aagacgaagc agtgcgggct 27960 tcctgaatgt tgcctcagct gaaagaccct ggcagctagt ttttatcata gagagaaaga 28020 caaaagaggt ggacaatggg tgaaaacgaa acaccacctt tctatattat tgcatcccct 28080 gaaggttgta catcacatca ccccccaggg tcccatggaa tcctatacta acttgattct 28140 gtacttctga gtagggtggg gttctaacct taggaactga atataagaac agtggaaaat 28200 aaagctagca gtgtttcaat ttacctagtt ggtaatttct ttcttgcttt ctagtttggg 28260 gtatggcttg ggtacatgaa agcagagccc agggtcttct gatggaaatg ttcccttatg 28320 atttgtgata ataatccaat gggaggagta catttccctg ctccatcagt gttgagcttg 28380 accgtgagac ttgctttagc caatgggatg ttagcagatg tgatgcaagc agaggcttga 28440 aacgtgcttg tggggctggg cttgccttcc agtcttttgc cctgaaaaga acatggtccg 28500 aggaagatga gtgacagatg gagcagacct agaccaacct gcaggcctga gcccagccta 28560 gatcaactga gctccatctg acctgtggac atgtgagaga gaaatagatg cttttgtgtt 28620 ctggggttgt tttgttacat aaaagtatga cagccacagc aactgaggca cgatctcagg 28680 agttggagcc tattgcttat gaacaaggtt aagagatcaa tttctgcttc ttactctttc 28740 aatttatacc gcccaaacca acactgattt gtctctctgg tcaccgaaaa gacaggtaaa 28800 aacatgggga tagatacaac accaaaagca tgatccacaa aagaaaaaaa agataaactg 28860 tacctcttta aaattaaaaa ctctgctctg ccaaagacac tattaagaaa atagaaacat 28920 ggccaagcgt ggtggctcac gcctgcaatc ccagaacttt gggaggtcga ggtgggtgaa 28980 tcaccagagg tcaggaattc gagaccagcc tggccaacat ggtaaaaccc tgtctcaact 29040 aaaaatacaa aaattagcca ggcatggtgg cgggcgcctg taatcccagc tactcgggag 29100 gctgaggcag gagaattgct tgaacccagg aggcggaggt tgcaatgagc caagatcaca 29160 ccattgcact ccagtctggg tgacaagagc aaacctctgt cttaaaaaaa aaaaaaaaga 29220 aaaagaaaaa agaaaagaaa agaaaagaaa aatgtgattc ccaagcttgt agaaaatatt 29280 tgcaaaagat atctctgatg aaggactggt atctgcaata tataaagaac tcttaaaacc 29340 caacaattaa aaaaaaccgt atctgctaaa atagctgaga ttcaaaacac tgatgacacc 29400 agatgctgag gaggatgtgg agcaacagga actctcattc attgctggtg ggaatgcaca 29460 acggtacagc cactttggaa ggcatctggc agtttattac caaactaagc ataacctact 29520 acacaatcca gcaattgtgc tcccatatga gttgaaaact tacgtctaca cacactcaca 29580 aaaatggcac atggatattt acagcagctt tattcataaa tgccaaaact tggaaacaat 29640 taagatgtcc ttcaataggt gaatggataa acaacttgtg gtatattcac ataatgggat 29700 attattcagc actaagaaaa aagagttgac caggtgcagg tgcagtggct cacacctata 29760 atcccagcac tttgggaggc taaggtggga ggattgtttg agcccagaag tttgagacca 29820 gcttgggcaa caagtgggac cccccccccc accatatcta caaagagtta aacatttagc 29880 tggttgtggt ggcatgcaac tgtggtccca gctacacagg aggctgaggc aggagaaaca 29940 cttgagccca ggagattgag gttgcagtga gccgtgattg taccactgca ctccagcctg 30000 11 20 DNA Artificial Sequence Antisense Oligonucleotide 11 tcgtcatcgt cttcatctcc 20 12 20 DNA Artificial Sequence Antisense Oligonucleotide 12 cctcagagcc atcgtcgtca 20 13 20 DNA Artificial Sequence Antisense Oligonucleotide 13 cctgaggtcc cctcagagcc 20 14 20 DNA Artificial Sequence Antisense Oligonucleotide 14 cagcccggat cctcgcagct 20 15 20 DNA Artificial Sequence Antisense Oligonucleotide 15 gggcagcccg gatcctcgca 20 16 20 DNA Artificial Sequence Antisense Oligonucleotide 16 tggatgtggg atccggcacg 20 17 20 DNA Artificial Sequence Antisense Oligonucleotide 17 tggctattag gccccggctt 20 18 20 DNA Artificial Sequence Antisense Oligonucleotide 18 atgtcctcag agcctgcctc 20 19 20 DNA Artificial Sequence Antisense Oligonucleotide 19 ttctggaagc tgaggtcttc 20 20 20 DNA Artificial Sequence Antisense Oligonucleotide 20 cccttctgga agctgaggtc 20 21 20 DNA Artificial Sequence Antisense Oligonucleotide 21 tagccctcct tccgggtggc 20 22 20 DNA Artificial Sequence Antisense Oligonucleotide 22 ctgatgccct tgaaaaacca 20 23 20 DNA Artificial Sequence Antisense Oligonucleotide 23 gcccagcatg ttgccgggag 20 24 20 DNA Artificial Sequence Antisense Oligonucleotide 24 aaggagccca gcatgttgcc 20 25 20 DNA Artificial Sequence Antisense Oligonucleotide 25 atgaaggagc ccagcatgtt 20 26 20 DNA Artificial Sequence Antisense Oligonucleotide 26 gatcatgaag gagcccagca 20 27 20 DNA Artificial Sequence Antisense Oligonucleotide 27 ccggatcatg aaggagccca 20 28 20 DNA Artificial Sequence Antisense Oligonucleotide 28 cggacaaaga gtagcttcct 20 29 20 DNA Artificial Sequence Antisense Oligonucleotide 29 cagggtccgg atcttgtaat 20 30 20 DNA Artificial Sequence Antisense Oligonucleotide 30 tcgttcccct tcttgtagtg 20 31 20 DNA Artificial Sequence Antisense Oligonucleotide 31 gacagtttct ggcagagccc 20 32 20 DNA Artificial Sequence Antisense Oligonucleotide 32 gacatgcagg gcaccgacag 20 33 20 DNA Artificial Sequence Antisense Oligonucleotide 33 ggcttggaag acatgcaggg 20 34 20 DNA Artificial Sequence Antisense Oligonucleotide 34 agctccaagt ttcttctcca 20 35 20 DNA Artificial Sequence Antisense Oligonucleotide 35 cccagctcca agtttcttct 20 36 20 DNA Artificial Sequence Antisense Oligonucleotide 36 ctgcccagct ccaagtttct 20 37 20 DNA Artificial Sequence Antisense Oligonucleotide 37 ggtggccatc cagacttccc 20 38 20 DNA Artificial Sequence Antisense Oligonucleotide 38 ttgttgtagg tggccatcca 20 39 20 DNA Artificial Sequence Antisense Oligonucleotide 39 tgtgcttgtt gtaggtggcc 20 40 20 DNA Artificial Sequence Antisense Oligonucleotide 40 tggtgtgctt gttgtaggtg 20 41 20 DNA Artificial Sequence Antisense Oligonucleotide 41 gacatgctcc ctggcttcat 20 42 20 DNA Artificial Sequence Antisense Oligonucleotide 42 ggaaggcctc caccgacatg 20 43 20 DNA Artificial Sequence Antisense Oligonucleotide 43 gctgcagagt tttcatcacg 20 44 20 DNA Artificial Sequence Antisense Oligonucleotide 44 aagtttgacc agcttgtcat 20 45 20 DNA Artificial Sequence Antisense Oligonucleotide 45 ctccgtgatg atgtagatgg 20 46 20 DNA Artificial Sequence Antisense Oligonucleotide 46 catcactttt cagaaagtcc 20 47 20 DNA Artificial Sequence Antisense Oligonucleotide 47 ctgcttgctg ccctcatcac 20 48 20 DNA Artificial Sequence Antisense Oligonucleotide 48 ggctgagaag tcaatgagtt 20 49 20 DNA Artificial Sequence Antisense Oligonucleotide 49 cttctgcaat ctgggctgag 20 50 20 DNA Artificial Sequence Antisense Oligonucleotide 50 tgccttctgc aatctgggct 20 51 20 DNA Artificial Sequence Antisense Oligonucleotide 51 aggccatgcc ttctgcaatc 20 52 20 DNA Artificial Sequence Antisense Oligonucleotide 52 tgctcgatga aggccatgcc 20 53 20 DNA Artificial Sequence Antisense Oligonucleotide 53 tagttcctct gctcgatgaa 20 54 20 DNA Artificial Sequence Antisense Oligonucleotide 54 tcggtggatg tagttcctct 20 55 20 DNA Artificial Sequence Antisense Oligonucleotide 55 tcagcaatct tacacaccag 20 56 20 DNA Artificial Sequence Antisense Oligonucleotide 56 gacccgggcc aggccaaagt 20 57 20 DNA Artificial Sequence Antisense Oligonucleotide 57 tcgttgtcct caatgacccg 20 58 20 DNA Artificial Sequence Antisense Oligonucleotide 58 aacttggccc cttcccgagc 20 59 20 DNA Artificial Sequence Antisense Oligonucleotide 59 gcttcaggag ctgtccactt 20 60 20 DNA Artificial Sequence Antisense Oligonucleotide 60 tctgacttga tggtgaagga 20 61 20 DNA Artificial Sequence Antisense Oligonucleotide 61 gggatccggc cgtaggtgac 20 62 20 DNA Artificial Sequence Antisense Oligonucleotide 62 ggtttgacat ccctgggtaa 20 63 20 DNA Artificial Sequence Antisense Oligonucleotide 63 catccggtat ccacgctcca 20 64 20 DNA Artificial Sequence Antisense Oligonucleotide 64 gcgcatcatg atgttgtaga 20 65 20 DNA Artificial Sequence Antisense Oligonucleotide 65 agcacactct ggatgtattc 20 66 20 DNA Artificial Sequence Antisense Oligonucleotide 66 tccagcacac tctggatgta 20 67 20 DNA Artificial Sequence Antisense Oligonucleotide 67 tcatccagca cactctggat 20 68 20 DNA Artificial Sequence Antisense Oligonucleotide 68 atggctgctg ttggtactgg 20 69 20 DNA Artificial Sequence Antisense Oligonucleotide 69 cctccctatc atggctgctg 20 70 20 DNA Artificial Sequence Antisense Oligonucleotide 70 ccttcgagcc accacctggg 20 71 20 DNA Artificial Sequence Antisense Oligonucleotide 71 cagtccaacc tacccactgg 20 72 20 DNA Artificial Sequence Antisense Oligonucleotide 72 ggattgcaag agtcaaaaag 20 73 20 DNA Artificial Sequence Antisense Oligonucleotide 73 gtcagattgt ggattgcaag 20 74 20 DNA Artificial Sequence Antisense Oligonucleotide 74 cctgagaatg tcagattgtg 20 75 20 DNA Artificial Sequence Antisense Oligonucleotide 75 gctgtaacta aaatccaacc 20 76 20 DNA Artificial Sequence Antisense Oligonucleotide 76 acagctgtaa ctaaaatcca 20 77 20 DNA Artificial Sequence Antisense Oligonucleotide 77 actattttga aagtttccct 20 78 20 DNA Artificial Sequence Antisense Oligonucleotide 78 tcatttcact attttgaaag 20 79 20 DNA Artificial Sequence Antisense Oligonucleotide 79 taagacttgc atttatatct 20 80 20 DNA Artificial Sequence Antisense Oligonucleotide 80 agatgtgcac caccatgctt 20 81 20 DNA Artificial Sequence Antisense Oligonucleotide 81 tgcaccaccc tatattatca 20 82 20 DNA Artificial Sequence Antisense Oligonucleotide 82 aacatacata ttaggctggt 20 83 20 DNA Artificial Sequence Antisense Oligonucleotide 83 gagtagcttc ctgaattgac 20 84 20 DNA Artificial Sequence Antisense Oligonucleotide 84 tcgttcccct ctggaacaga 20 85 20 DNA Artificial Sequence Antisense Oligonucleotide 85 gggtccttac ccatccagac 20 86 20 DNA Artificial Sequence Antisense Oligonucleotide 86 ggccagcaga agatgccaca 20 87 20 DNA Artificial Sequence Antisense Oligonucleotide 87 tttgacatcc ctgaaaagga 20 

What is claimed is:
 1. A compound 8 to 50 nucleobases in length targeted to a nucleic acid molecule encoding hematopoietic cell protein tyrosine kinase, wherein said compound specifically hybridizes with said nucleic acid molecule encoding hematopoietic cell protein tyrosine kinase and inhibits the expression of hematopoietic cell protein tyrosine kinase.
 2. The compound of claim 1 which is an antisense oligonucleotide.
 3. The compound of claim 2 wherein the antisense oligonucleotide has a sequence comprising SEQ ID NO: 13, 17, 18, 19, 20, 22, 31, 32, 33, 34, 35, 36, 37, 39, 40, 42, 47, 51, 53, 57, 58, 60, 63, 66, 67, 68, 69, 70, 73, 74, 79, 84, 86 or
 87. 4. The compound of claim 2 wherein the antisense oligonucleotide comprises at least one modified internucleoside linkage.
 5. The compound of claim 4 wherein the modified internucleoside linkage is a phosphorothioate linkage.
 6. The compound of claim 2 wherein the antisense oligonucleotide comprises at least one modified sugar moiety.
 7. The compound of claim 6 wherein the modified sugar moiety is a 2′-O-methoxyethyl sugar moiety.
 8. The compound of claim 2 wherein the antisense oligonucleotide comprises at least one modified nucleobase.
 9. The compound of claim 8 wherein the modified nucleobase is a 5-methylcytosine.
 10. The compound of claim 2 wherein the antisense oligonucleotide is a chimeric oligonucleotide.
 11. A compound 8 to 50 nucleobases in length which specifically hybridizes with at least an 8-nucleobase portion of an active site on a nucleic acid molecule encoding hematopoietic cell protein tyrosine kinase.
 12. A composition comprising the compound of claim 1 and a pharmaceutically acceptable carrier or diluent.
 13. The composition of claim 12 further comprising a colloidal dispersion system.
 14. The composition of claim 12 wherein the compound is an antisense oligonucleotide.
 15. A method of inhibiting the expression of hematopoietic cell protein tyrosine kinase in cells or tissues comprising contacting said cells or tissues with the compound of claim 1 so that expression of hematopoietic cell protein tyrosine kinase is inhibited.
 16. A method of treating an animal having a disease or condition associated with hematopoietic cell protein tyrosine kinase comprising administering to said animal a therapeutically or prophylactically effective amount of the compound of claim 1 so that expression of hematopoietic cell protein tyrosine kinase is inhibited.
 17. The method of claim 16 wherein the disease or condition is a hyperproliferative disorder.
 18. The method of claim 17 wherein the hyperproliferative disorder is cancer.
 19. The method of claim 18 wherein the cancer is leukemia.
 20. The method of claim 16 wherein the disease or condition is selected from the group consisting of inflammation, diabetes and viral infection. 